Starting pathology

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Starting Pathology - front page.png
Author: Mikael Häggström, M.D.

This is a handbook directed at new pathology trainees (mainly residents or trainees with medical doctor degrees or similar).

Copies and prints

To get a printable version of this resource, go to, click Starting pathology (handbook), and click Printable version in the left hand menu. For best print results, use a color printer and color printer paper, or google a "copy shop" for a color print delivery or in-store pickup (possibly as a photo book, otherwise you can keep them in a binder).

This resource is released under the Creative Commons Attribution 4.0 International (CC-BY 4.0) license, meaning that if you reuse any of its content (such as in scholarly articles), you need to mention its author (Mikael Häggström, M.D.). Also, many images are Public Domain, that is, without any restrictions. The status of each image is seen on its description page (found by clicking the image at Furthermore, tables and graphs are never copyrightable unless they have some artistic, literary or other copyrightable aspect.[1] 


To contact the page creator/author, write a message to mikaelDot.svghaeggstroemArobaze.svgnuvancehealthDot.svgorg.

Please give feedback on any errors that you encounter in this resource, as well as pertinent omissions that you feel should be there. Preferably, contribute yourself: See the Contribute page at

Learning pathology

  The goal of this resource is to make a new pathology trainee able to properly handle at least 70% of cases that are expected at an average general pathology department, including the exclusion of the most pertinent differential diagnoses thereof. Its aim is to present you at least one way of doing things that is at least adequate for a particular situation, so that although there may be various routines at various locations, adherence to these methods should not result in a worse reprimand from a senior than "although that was adequate, that is not how we do it here". Still ask for help whenever needed, such as first time you are doing something, or whenever you are not sure about what to do, especially when doing something potentially irreversible.

What a pathologist needs to memorize

The best method for memorization is generally through repeated exposure in everyday practice, and the scope thereof will depend on your eventual location and subspecialty, and you will eventually forget everything else, more or less. Yet, the following things are most important for a pathologist trainee to focus on memorizing:

  • Emergent pathology, mostly relating to intraoperative or frozen section consultations. This includes information that usually cannot be timely looked up on the Internet when needed.
  • Main pitfalls: The most common and dangerous situations where a pathologist may not recognize the need to look something up further or ask a senior colleague, or where a significant risk of diagnosis error remains after doing so.
  • Interpretation of non-written results, including patterns and signs which can be seen grossly or under the microscope. It confers the ability to translate visuals and other more or less non-verbalizable information into words that can be looked up if needed, and conceive the most likely diagnoses based on both describable and more abstract appearances.
  • Proficiency in diagnosing equivocal or borderline cases where readily available sources and evidence usually deal with discrete and specific disease entities and subcategories thereof. Unusual or equivocal presentations of very common diseases and conditions are still generally more common than rare diseases, and constitutes a major workload in everyday pathology practice. However, most textbooks still give disproportionately large room for rare diseases compared to such presentations. Nevertheless, strive to master the common conditions (including the most common pitfalls) before diving into the uncommon. After all, you will get by with effectively handling the regular cases wherever you work, so that you will have time to study or ask others for unfamiliar cases, as long as you know your pitfalls, and have an idea about your unknowns:
  • Having an idea of one’s unknowns; being aware of a lack of knowledge in unfamiliar fields. For example, a pathologist generally does not need in depth knowledge about diseases that are generally sent out to specialized centers (such as pediatric musculoskeletal oncology), but just enough to be able to suspect such diseases. In the same manner, a pathologist needs to have an idea of the optimal limits of practice, between what should optimally be handled personally by the pathologist and what is better handled by others, including senior colleagues, technicians, pathology assistants, junior colleagues and artificial intelligence.
  • Where to find information for various situations. It includes which person or which search engine is most useful for various clinical situations. See the Using resources section below for further information. Similarly, a pathologist often needs to be efficient at finding what is relevant among a large amount of information, and be able to integrate it into a decision or a relatively short report. For questions where a look-up does not readily give the answer, a new trainee usually gets satisfactory replies even from senior trainees, but the more experienced you get, the more you need to establish contacts with particular people, such as certain subspecialties, who are most likely to be able to answer your questions when needed.
This resource aims to cover what you need to memorize as a first year pathology trainee.
  • How to distinguish memorization-worthy versus look-up versus practically useless information. With the ease of access to pathology information on the Internet through smartphones and computers, those studying for the everyday practice as a pathologist should not waste time memorizing what can essentially always be conveniently and timely looked up when needed. This includes most of the content of books and web pages that are sorted by names of diseases and conditions, because if the name of a disease is already known, then it can relatively quickly be looked up when needed in such sources. When finding relevant look-up information on the Internet or local repositories, it is generally enough to remember enough of its related words in order to find it again. After all, other doctors and even laypersons can look up diseases and conditions themselves, without the need for a pathologist consultation, so the expertise of memorizing such readily available information is expendable. Similarly, electronic systems are better suited than the human brain for the storage and rapid retrieval of databases of for example immunohistochemistry and genetics results of various diseases. The topics listed in this section are already immense enough to cover a lifetime of learning. Learning pathology therefore optimally involves the memorization of where and how to find look-up information, rather than directly memorizing such information. Therefore, if you need to choose a textbook to study, then choose one that you will always be able to quickly reach through your smartphone whenever you need its look-up information. Accordingly, the final aim of this resource is to help pathology trainees to give accurate and clinically useful reports to clinicians, in synergy with the resources that are available in everyday pathology practice, and to establish routines to continue such practices. The intended end result is to help clinicians to improve the lives as much as possible to as many people as possible, even if it means forgoing the prestige of becoming a walking encyclopedia. It also means finding high-yield learning sources, for even if they may take longer time to find, you will be better prepared for real life than when you study low-yield knowledge, which includes statistics that is very unlikely to be used diagnostically, mainly because their calculations would be so complex that it is not worth it. For example, in reality you generally have a pattern of signs and other findings and you want to know the likelihood of each differential diagnosis, and for this purpose you only get limited help by knowing the reverse likelihood of what percentage each individual condition is to display the finding, because it would still be necessary to also know for example the epidemiology of each disease to calculate its likelihood. Instead, the optimal studying is generally not of diseases individually, but rather of patterns of signs and other findings and the likelihoods of each differential diagnosis thereof. Arguably the best method of acquiring such knowledge is to be involved in many real cases at a pathology department, making your own diagnostic thinking of them, and correcting your thinking based on how you differed from a senior's report. The next best method is arguably to solve virtual cases such as found in pathology qbanks.
  • How to efficiently study for exams that contain questions that require direct memorization of look-up (or even practically useless) information, as long as such exams are in the way of practicing pathology. The best approach is arguably to spend enough time and effort on memorizing what is memorization-worthy, to the point where you will pass an exam even if you will fail multiple questions that require memorization of look-up or practically useless information. However, when starting pathology training, do not focus on studying for any final exams that are years away, because the content on such exams is systematically very different from what you need to know initially. For instance, you initially need to know how to handle the common types of cases, but exam makers on the other hand, in their effort to distinguish those who have studied more extensively than others, will systematically choose presentations that are not commonly encountered.  Further exam advice is found in the Secrets chapter at
Type of information Examples (usually) Learning approach
  • Emergent matters
  • Pitfalls
  • Interpretation of non-written results
Directly memorizing it.
  • Textbooks and websites organized by names of diseases and conditions
  • Immunohistochemistry results
  • Associations between genetic mutations and diseases, and related molecular biology.
  • Classifications such as cancer staging
  • Large tables and diagrams
  • Long lists
Knowing where to find it when needed, and how to use it.
  • Diseases individually
Instead studying patterns of findings and signs, and how they support various differential diagnoses.
Practically useless
  • History
  • Most of scholarly articles
  • Most clinical management
Avoiding, or skipping to potentially useful parts.

Whether any piece of information is useful versus useless depend mainly on:

  • The likelihood of a situation where the information is useful.
  • The benefit versus detriment of having versus not having the information at hand in such a situation.

The clinical management aspects that can be useful for pathologists to learn are the thresholds for pathologic findings that substantially change the clinical management, such as a cancer stage that determines whether clinicians will try to completely remove all tumors versus treat palliatively. With such knowledge, pathologists can put relatively more effort on the cases and parts thereof that make the most difference to the patient. Otherwise, clinical management knowledge is generally useless to a pathologist.

Lectures may be memorization-worthy depending on the content, but a lecture of look-up-information is practically useless unless you maintain a system to quickly retrieve the information when needed. Thus, sometimes, it is better to study something more memorization-worthy while pretending to listen to a lecturer.

Also keep in mind that pathology in our look-up era is mainly a processing work rather than a memorization one, since your most important skills are to interpret findings, and sometimes involve a vast amount of information in order to suggest the most likely diagnoses. Again, arguably the best method fur such purposes is solving real or virtual cases.

Using resources

This resource is written with the intention to teach you what to do in the most common situations you are expected to encounter during your first years of pathology training, at least until the point that you are usually fairly confident about what disease or condition you have at hand, because then you know what words to use to look it up in the vast literature out there. At that point, the fastest way to get more information is generally by Googling the disease or condition name, followed by pathology outlines (which is generally the most likely to quickly give you the information you need), since Internet will always be readily available in pathology.[note 1] The most efficient method of studying to solve a case at hand is to not read articles in their entirety, but to scroll directly to the parts that are most likely to give you the information you need (generally past the first half of Pathology Outlines articles).

Specific search methods for some specific purposes include the following (and the author has no financial or other conflicts of interests in mentioning any of these):

  • Google, and then clicking the Images tab, if you just want to see more micrographs of the disease or condition. Even when you don't have a clue what condition you are looking at, you may find something that looks similar to your case by entering words you would use for the microscopic findings that you see.
  • Adding staging in Google searches for definitions of cancer stages, for example Googling prostate cancer staging. The first search will then generally be the one from the American Society of Clinical Oncology.
  • Considering a subscription for ImmunoQuery[notes 1] (or equivalent database if you find one) in order to generate the most pertinent immunohistochemistry stains when you have two or more differential diagnoses for a case at hand. It is not sufficient to just memorize a few usually positive or negative immunostains for each disease and condition, because what you need in reality is to figure out what immunostains to order so that you can pinpoint one diagnosis among your multiple differentials. To master that, you will need to memorize a vast amount of immunostains and at what percentages they are positive for a vast amount of diseases and conditions, or you can have an online service like ImmunoQuery do that work for you. After all, in pathology there is essentially no immunohistochemistry that is so emergent that you do not have the time to use a computer or smartphone to look it up.
  • ClinVar to look up the pathogenicity of specific genetic variants/mutations.

If the above resources do not provide a sufficient answer:

  • Googling what you are looking for. You may add the word pathology or equivalent if results are too clinical or layman-oriented. Before even reading the title of results, first look at the URL. If it is from a reputable organization then you may proceed to check if the title is pertinent to what you are looking for, but if it is from an unfamiliar site then you should only proceed if you don't find a better source among your search results, and you will need to look for additional proof of reliability such as authorship of the content in order to use it in the diagnostics of any case. You can generally rely on more articles for presumably well-established topics (such as anatomy, and relatively common diseases) than for potentially controversial and experimental topics, in which case you generally need to ask yourself if the author has a conflict of interest.

Ask a colleague at least whenever your own memory or a resource search is not enough, and there is a significant risk that you may do something irreversible that will negatively affect a patient.

Regarding lectures and knowledge your colleagues will tell you, make a judgment for each piece of information if it fits a criterion for memorization, or if it merits being written down somewhere you can find it so that you can look it up when needed.

Wikipedia often shows up among top Google results, and is generally accurate.[2]

Whenever possible, use textbooks and other sources that you can quickly access online, because you will likely always be close to the Internet, but not always close to your collections of physical material. Keep in mind that for the vast majority of content, you only need to have a hunch of where to find it again when needed, or what search terms to use. If something may be difficult to find again, you may add it to a personal digital collection to be readily available in times you need it.

Strive for sources that, taken together, are comprehensive enough for the presentation at hand. For example, if you first look in a resource on only benign conditions that may cause your presentation, you generally need to look for another source that includes malignant conditions as well.

Generally skip any part that tries to explain a microscopic appearance using only words, since a Google image search is generally more useful.

Test question

A 4 year old girl with a renal mass
Histopathology of Wilms' tumor, original.jpg
Histopathology of Wilms' tumor, annotated.jpg

You are a new resident at a community hospital that is closely affiliated with a university hospital. The attending gives you a couple of slides from a case that is not yet signed out to preview and then come back with what you think would be the next steps. You are also told to share them with a med student who rotates at the department. One of the cases is from a kidney of a 4 year old girl. You look up the patient's history and she was admitted for orthopedic care for multiple fractures, and CT incidentally found a kidney tumor where workup was initiated as an inpatient. Microscopy shows the image at right. The med student has a smartphone and by googling "common kidney tumors in children", Wilms' tumor (also known as nephroblastoma) shows up as one of the top choices. You look up the condition on Pathology Outlines and the case seems to fit the microscopic description with its 3 typical components (second image at right).[3] On the same web page you also quickly see the following pieces of look-up information:

  • Risk classification systems, where for example "COG intermediate risk" requires favorable histology and no evidence of anaplasia.
  • That there are no specific/diagnostic laboratory findings.
  • A bunch of associated genetic changes (WT1 (11p13), CTNNB1 (3p22), IGF2 (11p15), TP53 (17p13), MYCN (2p24), and 1q gain).
  • A bunch of associated immunohistochemistry results in the tumor, related non-neoplastic tissue, as well as in notable differential diagnoses (WT1, PAX8, vimentin, CD56, CD57, cytokeratins, EMA, desmin, cyclin D1, BCL2, CD34, myogenin, MyoD1, INI1, Glypican 3, AMACR, CK7, melanocytic markers (MelanA, HMB45), BRAF V600E, TFE3, TFEB, BCOR, and FLI1)

Which of the following would be the best next step if you were to decide yourself?

  1. Diagnosing Wilms' tumor, COG intermediate risk, based on the shown microscopic view alone.
  2. Look at the complete blood count for diagnostic findings.
  3. Order genetic testing for WT1 (11p13), CTNNB1 (3p22), IGF2 (11p15), TP53 (17p13), MYCN (2p24), and 1q gain.
  4. Order immunohistochemistry for WT1, PAX8, vimentin, CD56, CD57, cytokeratins, EMA, desmin, cyclin D1, BCL2, CD34, myogenin, MyoD1, INI1, Glypican 3, AMACR, CK7, MelanA, HMB45, BRAF V600E, TFE3, TFEB, BCOR, and FLI1.
  5. Say "I don't know" and ask for help.
Correct answer
Say I don't know and ask for help.png

A major skill of a pathologist is having an idea of one’s unknowns. Furthermore, pediatric oncology is generally outside the limits of independent practice of any individual pathologist, generally requiring at least consultation with a colleague before diagnosis, classification and decisions about further workup (which in this case may be made at a pediatric oncology center). Thus, even if you though you knew how to proceed on your own, saying "I don't know" and asking for help is still the most correct as a new resident for a case like this.
Incorrect answers

You can skip reading these if you are already agree with the explanation above.

  1. Although the microscopic view that is shown is enough to diagnose Wilms' tumor, it is not enough to classify it as COG intermediate risk without first having looked at the entirety of the microscopy slides to exclude evidence of anaplasia.
  2. There are no specific/diagnostic laboratory findings of Wilms' tumor.
  3. A senior or specialist consultation would be needed in order to find out which genetic tests would actually be worth performing in this case, even after reviewing the history or asking a clinician for any suspected syndrome associated with Wilms' tumor.
  4. The choice of immunohistochemistry panels should be based on which ones most efficiently distinguish the possible differential diagnoses of the case at hand, and not just which ones are associated with the lead diagnosis. As with genetic testing, a senior or specialist consultation would be needed in order to find out which immunohistochemistry tests would actually be worth performing in this case.  

Using this resource

In this resource, it is recommended to read attentively until the end of the emergent pathology section. That part can be regarded as mainly describing concepts, which are relevant to read through and understand or at least consider. The rest will mainly provide guidelines for various situations, such as when you are presented with a biopsy of the gastrointestinal tract. Memorization-worthy information will generally be highlighted by: Memorization-worthy: , otherwise it is recommended to scroll quickly through such situation-based chapters, just to get an idea of what kind of information is available there, and then keeping this resource at a known location for whenever you are in that situation.

  • Memorization-worthy:  This resource is available open-access and ad-free by googling patholines and then Starting pathology (handbook).

This resource is aimed at presenting the most important knowledge that you will need when starting pathology. For further knowledge that you will need as a pathologist and any subspecialization, the best way is to learn from reality, by solving the cases and problems that get presented to you, and thereby look specifically for the information that you will need among the immense literature and other information that is out there.

Also, this resource assumes that you use additional sources when needed (such as The WHO Classification of Tumors or others in the Using resources above). Therefore, it will not simply repeat such information, but may display external links to further information.

This resource also assumes that you will ask a colleague for advise if you see an unfamiliar presentation, and any literature lookup thereof still does not explain it. Therefore, this resource will focus on the most common presentations and the main differential diagnoses thereof, which may include rare conditions if for example the clinical management thereof would be significantly different. On the other hand, most rare conditions that generally have distinct presentations will be omitted. Therefore, keep in mind that there are many such rare conditions that you do not know about, so keep asking colleagues whenever a presentation remains strange to you.

Be tolerant to encountering many repetitions of the same content in related articles, since for example a cervical biopsy and a cervical cone have similar microscopic evaluation.

Using question banks

To test your knowledge on memorization-worthy information, seek questions that present you with a possible real life situation, as well as all pertinent information you can readily look up before needing to answer the question, so to ensure that it tests you on pertinent information as per the items earlier in this chapter. On the other hand, don't waste time on questions whose answer requires memorization of look-up or practically useless information (except if you want to practice looking up the answers online). There are about 5000 questions in PathPrimer, PathDojo and BoardVitals combined, so you can be picky about what questions to focus on.

Consider the usefulness of each question before spending significant time memorizing its answers or explanations, in order to maximize the useful knowledge you will learn overall. Generally, skip questions that test you on look-up information and practically useless information. Whenever you have a question where you can not picture in what real life situation it would be relevant to remember, then you can generally assume that it never will be. For questions that consists of a useful item together with a more useless one, only learn the the useful part and move on. If you can, flag/mark questions on memorization-worthy information that you did not know, and move on fairly quick on those as well, and later revisit those questions specifically if you have the time, as repetition is generally more efficient than lingering.

A common sign that a question will deal with look-up or practically useless information is where it asks which of the alternatives is false or correct for one particular condition, and the alternatives are relatively heterogenous (such as one dealing with diagnosis and another one dealing with prognosis). The high prevalence of such questions is mainly because they are easy and quick create, because the question creator can simply look up a condition, choose some more or less random facts, and then change small details to create alternatives. It requires no real life experience in everyday pathology practice, and learning from such a question is hence generally not useful for that purpose either. The thought processes of real life pathology is generally the opposite of this, because you are generally presented with a specific location, gross appearance and microscopic appearance, and you need to practice on finding the most likely causative condition thereof among many differential diagnoses. Even other kinds of memorization-worthy pieces of information generally have a more limited scope among alternatives (like knowing the optimal staining duration in hematoxylin for a frozen section among alternative durations (see Emergent pathology). Thus, to practice your knowledge in memorization-worthy pathology, it is generally most efficient to skip false-versus-correct questions, in order to spend your limited time on something more worthwhile. Similarly, questions are in general rather low-yield whenever they deviate from the realistic direction.

Other signs of unrealistic and therefore rather low-yield questions include those that mention what kind of test identified the condition, but does not give you the test result (such as a case presentation that includes "Serology identified the organism").

If you have gone through all 5000 questions of the main question banks, and still have plenty of time for a second round, then you may work on lower yield questions as well. For example, you may practice on looking up answers for look-up questions, unless the presentation makes it clear that you cannot timely and conveniently do so (such as being in a rush during a frozen section).

Test question

A question on a question

You want to practice your memorization-worthy knowledge in real life pathology and not for exams ( as per the Secrets chapter at You find the following multiple choice question: "Which of the following statements for squamous cell carcinoma (SCC) of the skin is false?"

  • For staging of SCC of the of the head and neck, pT1 corresponds to a diameter ≥ 2 cm and < 4 cm (this is the false alternative, as this defines pT2, whereas pT1 is defined as ≤ 2 cm)[4]
  • Most patients have a favorable outcome after surgical resection.
  • It occurs most often in sun exposed areas.
  • It often presents as a hyperkeratotic scaly plaque.
  • Microscopy typically shows carcinoma of keratinocytes that infiltrates the dermis.

What is the most efficient way of dealing with this question for real-life pathology practice?

  1. Choosing an answer, then thoroughly reviewing each alternative, as well as the question explanation.
  2. Like the first alternative, but only if you answered the question wrong.
  3. Only carefully review the single association you need to answer the question correctly (in this case, that for SCC of the skin, pT1 is defined as ≤ 2 cm).
  4. Skip this question and move on.
Correct answer

Skip this question and move on.png
The answer alternatives of this question are all over the place (a mix of prognosis, location, staging, gross description and microscopic description), which usually means that it was created by just looking up the condition in a resource and picking information from there, resulting in a collection of what is usually just look-up information.

Incorrect answers

You can skip reading these if you are already agree with the explanation above.

1 and 2. These are waste of time.
3. If this was a question of memorization-worthy information, or if you were studying for an exam, this would generally be the correct answer. However, staging of cancers can essentially always conveniently and timely be looked up when needed, so this is not memorization-worthy for everyday pathology practice.


General advice


1. More invasive intraoperative consultations
(such as open surgery)
2. Less invasive intraoperative consultations
(such as skins)
3. Fresh lymph nodes
4. Fresh breast tissue (should be in
formalin within an hour from surgery)
5. Other fresh tissue
6. Tissue in formalin

  • When making a mistake, admit that you did it and learn from it so as to focus on not repeating it.
  • Say "I don't know" instead of making up answers for what you do not know.
  • Try to fit findings with the clinical picture, in order to make a report that makes sense, but do not make up findings that you do not see, and do not omit potentially relevant features just to fit an expected story.
  • Ask for help whenever needed, such as first time you are doing something, or whenever you are not sure about what to do, especially when doing something potentially irreversible. Also ask for help in moments whenever there is a high risk that you will not achieve what you need to do within a clinically acceptable time. For prioritizing when you have more than one thing ongoing at the same time, the list at right can be used. Still, before asking, try to do as much as you can, as long as you do not do anything potentially irreversible, so that you can evaluate how you did it compared to the standard, and thereby know better how you will do it next time.
  • Do not wait for the whole pile. Whenever you can, do not be idle or do less urgent work while there is a pile of more urgent work gathering for you elsewhere. Instead, be familiar with where such piles are forming, and go there and grab whatever you may start working on right away.
  • For larger specimens that need fixation before final grossing, you can still start writing a report of measurements and other externally visible findings to save time for later.
  • Save your digital reports frequently.

Emergent pathology

  Memorization-worthy:  Information relating to emergent pathology is often not conveniently and timely looked up when needed because of the need for a fast report.


Frozen sections

Even new pathology trainees may end up being the first responders to frozen sections (as well as intraoperative consultations by gross inspection only).


Prepare at least the following:

  • Finding out which senior to call for help if responding to a frozen section. A fairly new pathology trainee should generally not independently make a report to the referring physician without having at least consulted with a senior, and therefore the diagnostics of frozen section slides is not included in this section. In the meantime, ensure that you have a working smartphone available, and know beforehand who to contact whenever you are at risk of being responsible for a frozen section, so that you can perform micrography of the slide in case and send it to the senior if that person can not be physically present within an acceptable time.
Main sites of metastases for some common cancer types. Primary cancers are denoted by "...cancer" and their main metastasis sites are denoted by "...metastases".[5]
  • If possible, look up pertinent medical histories of potential cases that may appear as frozen sections or other forms of intraoperative consultations. For example, surgery departments may have schedules of patients for the day that you will cover frozen sections. On such lists, types of surgeries that often come as intraoperative consultations mainly include potentially malignant skin excisions, lung excisions (larger than biopsies), ovarian tumors, and samples from other common metastasis sites (lungs, liver, brain, bone). The most important details to find out are:
  • What you may do yourself if you will be alone when you get the specimen, or if you need to wait for particular seniors before doing potentially irreversible steps such as inking and sectioning.
  • Previous biopsies. For expected excisions from common metastasis sites, look thoroughly for any past cancer diagnoses. Note the pathologic diagnoses of the biopsies((, as well as the collection dates and accession numbers.))
  • Tumor sizes where applicable(, and whether the estimation was from imaging or microscopy).
  • Make sure you have a working microtome. Switch its blade if you are not certain it has had limited use.
  • Prepare at least as many chucks as you think you will need according to any surgery schedule (or at least 3 of preferably various sizes).

(If you don't have a conductor, or if the embedding medium completely hardened before you applied it, perform cryotomy of the embedding medium to get a larger and smoother top.)

  • Inspect the H&E staining containers and refill if necessary.
  • Ensure that you have frozen section medium, as well as cover slips and mounting fluid.

Performing frozen sectioning

  • Inform relevant seniors.
  • Look at any requisition form or otherwise check or confirm what answers the requesting clinician wants. When the histopathologic type of tumor is known from before and its distance to the closest margin is relatively far, a gross intraoperative consultation is generally enough to measure that distance.
  • Measure the size of the specimen.
  • If you are permitted to proceed with the following steps, which are potentially irreversible, still consider whether there are any surprising aspects that requires you to wait until a senior arrives.
  • Ink relevant margins
  • 'Section the specimen so as to be able to see relevant pathologies, and closest distances to relevant margins.
  • Select tissue to be able to answer the clinician's questions.
  • Trim samples to make them equally thick, since you will need to section away more from thick pieces before thinner pieces will appear in cryotomy slices.
Minimal time in solutions for frozen sections.

Test question

Hematoxylin in frozen sectioning

You are put on frozen sectioning duty, and a specimen arrives. You inform the attending over the phone, who will require a moment to reach the room, and therefore tells you to prepare two microscopy slides in the meantime. You make sections, but the note that instructs the number of dips or duration in the hematoxylin solution has become unreadable due to a hematoxylin stain. You don't have any phone signal in the frozen section room, so you don't have time to look it up. To what extent will you put the slide in the hematoxylin solution?

  • A. 1 minute and 30 seconds
  • B. 1 dip
  • C. 10 seconds
  • D. 5 dips

Time in hematoxylin solution.jpg


This is generally the minimal time required for proper hematoxylin staining during frozen sections. Yet, if you know the solution is not expired or diluted, and you are really in a rush, then you can possibly have it acceptably stained in 1 minute in hematoxylin.


Problem Cause Solution
Tissue cracks off in cryotomy
  • Block too cold
Repair by warming slightly and adding embedding medium
Thick and thin slices
  • Inconsistent clamping
  • Dull blade
  • Incorrect blade angle
  • Ensure block holder and blade holder are tight
  • Change blade
  • Correct knife angle
Wrinkled, compressed or puckered sections
  • Dirty or dull blade
  • Tissue too warm
  • Clean blade
  • Move or replace blade
  • Cut tissue at colder temperature
Tissue advances but does not cut
  • Inconsistent clamping
  • Ensure blade holder is tight
Sections roll up
  • Anti-roll plate is not adjucted correctly
  • Readjust anti-roll plate
Sections thaw on the blade
  • Blade is too warm
  • Cool the blade
Sections stick to the anti-roll plate or blade
  • Static in the cryostat
  • Apply anti-static spray or anti-static gun
Sections split vertically
  • Dirt or nick on blade
  • Clean, move or replace blade
Sections have fine cracks parallel to the blade edge
  • Too cold temperature
  • Warm the tissue
Sections show signs of vibrations
  • Specimen too loose
  • Incorrect blade angle
  • Tighten chuck to the holder
  • Change the blade angle
Stain is dull and muddy
  • Drying artifact
  • Put sections on glass slides immediately in fixative

Suspected malignant skin excisions

While most frozen sections can be predicted from schedules of the operating room and thereby be looked up beforehand, suspected malignant skin excisions often come from outside the main surgery department, even more indicating memorization of how to handle them.

Tissue selection
Tissue selection from suspected malignant skin lesions, by lesion size:[6][notes 3]
<4 mm 4 - 8 mm 9 - 15 mm
Tissue selection from skin excision with less than 4 mm suspected malignant lesion.png Tissue selection from skin excision with 4-8 mm suspected malignant lesion.png Tissue selection from skin excision with 9-15 mm suspected malignant lesion.png

In table above, each top image shows recommended lines for cutting out slices to be submitted for further processing. Bottom image shows which side of the slice that should be put to microtomy. Dashed lines here mean that either side could be used.  

Other frozen sections

Although these are generally given on schedules of the operating room, any pathologist may end up suddenly covering for another one, and subsequently be presented with the frozen section case without having had the time to look it up beforehand.

In malignant or suspected malignant cases, surgical margins are generally more important than main tumor diagnosis.

  • In lung wedge resection and lobectomy, sample the surgical margin that is presumably closest to a tumor for frozen sectioning.  
  • In an intestine with tumor, it is generally enough to open the intestine (avoiding cutting through a tumor unless it is corcumferantial, and grossly measuring the distances to the proximal and distal surgical margins, as well as the distances to the radial or mesenteric surgical margins.  
  • For a donor kidney biopsy, generally evaluate as per local protocol.  


  • Call the requesting clinician
  • Verify that you are talking to that person, or someone who can immediately convey the diagnosis to that person
  • Tell the patient identity (with at least two different identifiers, such as name and date of birth)
  • (Ask for a readback of your diagnosis)
  • State your diagnosis
  • (Make sure the clinician reads the diagnosis back to you.)


  • Hello, this is from pathology. I have a frozen section result for Dr. (name of the clinician)
  • This is Dr. ____, and I have a diagnosis on (patient name and date of birth)(, so if you could please read back to me after,) the diagnosis is (diagnosis)





Adipose tissue with crumpling artifact due to insufficient fixation.

Within an hour after removal from the body,[7] tissue samples should generally be placed in vessels with enough fixative to allow them to lie freely in the solution.[8] The standard fixation fluid is generally 10% neutral buffered formalin, which is roughly equivalent to 4% formaldehyde.[9] The ratio of tissue:formalin should be 1:5[10] to 1:10[11].[11]


The duration depends on tissue thickness, where formalin will penetrate and fix the tissue at ~1 mm/hour.[12]

When not to use formalin

The main exceptions to using formalin are mainly:

  • A tophus or other specimen suspicious for gout versus pseudogout should be sent in alcohol or dry, since formalin will dissolve the crystals.
  • Lymph nodes (or other lymphoid aggregates) with a suspicion of lymphoma, where samples are generally put in a special solution for flow cytometry.
  • Products of conception with a need to take samples for genetic testing.

Gross processing

  Following are general notes on selection and trimming in pathology.  

Before cutting

  • Confirm that the patient identity on the specimen container matches the identity that will be applied to the gross description and cassettes. {{If the referral or requisition form is available, confirm the patient identity on that one as well.}}
For unclear or potentially ambiguous handwriting (here "Right" or "Left" renal stone), look at the referral or requisition form ((and the medical record if available)).
  • (Check for any discrepancy between the specimen description on the container and on the referral or requisition form, such as left versus right.)
  • Don't omit any piece in the container, such as ones hidden in wraps.
  • Generally measure in 3 dimensions, or in volume, but the greatest dimension is generally enough for specimens less than 0.4 cm.
  • Generally weigh entire organs, after having any attached tissue trimmed away if feasible.
  • (Note the color of the sample, even when unremarkable, but do not linger on deciding it.)[notes 4]
  • Generally, use inking for resection margins where cancer radicality is important.  
  • (On fatty or greasy surfaces, apply vinegar to emulsify and remove the fat, dry the specimen and then ink. Otherwise, vinegar can be used either before or after inking to "dry" it.)
  • (Preferably photograph or make a drawing where slices have been taken.)[13]
  • Remove any surgical stitches from samples before microtomy.
  • (At least for larger samples, consider looking for medical imaging or biopsy reports in order to better guide the process.)[14]
  • Fix bone in formalin prior to decalcification. Use reminders so not to forget bone that is decalcifying.


  • When cutting with the longer knives, try to cut in one stroke - do not use like a saw (continuous back and forth)
  • Generally, strive to make slices perpendicular to visible interfaces of relevant tissues.
  • Generelly dissect and inspect the entire specimen, while keeping relevant parts intact enough for presentation to seniors and/or maintaining orientation.
  • Trim tissues for microscopy examination to a thickness of maximum 3-4 mm.[notes 5]

Perpendicular versus en face sections

Perpendicular and en face sections

Two major types of sections in gross processing are perpendicular and en face sections:

  • Perpendicular sections allow for measurement of the distance between a lesion and the surgical margin.
  • En face means that the section is tangential to the region of interest (such as a lesion) of a specimen. It does not in itself specify whether subsequent microtomy of the slice should be performed on the peripheral or proximal surface of the slice (the peripheral surface of an en face section is closer to being the true margin, whereas the proximal surface generally displays more area and therefore generally has greater sensitivity in showing pathology, also compared to perpendicular sections).
  • A shaved section is a superficial en face slice that contains the entire surface of the segment.

Tissue selection

When sampling sections to submit for microscopic examination, whenever you sample from something that looks abnormal, generally try to also sample from the same type of tissue that looks normal.[notes 6]

Biopsy wraps, bags and sponges

Items used for submitting specimens: (Biopsy) wrap, (biopsy) sponge, (tissue processing) cassette and (biopsy) bag.

Put the following types of specimens in bags:

  • Tiny specimens that need to be poured out from their containers.
  • Bloody specimens such as endometrial curettages or products of conception. For products of conception, chorionic villi may otherwise contaminate other specimens. Bloody specimens may stick to wraps, so generally avoid that situation.
  • Friable tissue such as urinary bladder biopsies.

Put the following types of specimens in bags, wraps or sponges:

  • Other tiny specimens
  • ((Any small piece of tissue where there is no leftover specimen to retake sections, since tissues occasionally get lost from cassettes, and the absence of a wrap, sponge or bag in the cassette of such cases points towards a mistake made at gross processing.))

Specimens must be fixed enough to be put on sponges.

H&E staining urgency

(Even in departments where other staff are primarily responsible for determining the urgency of H&E staining of each specimen, still double-check that it is correct if you can, such as by cassette color.) A major indication for rushing cases through H&E staining is a high risk of cancer, especially where immunohistochemistry staining will likely be performed, and the decision and types of staining will be determined by the standard H&E stain. Tissues that are generally rushed are:

  • Brain biopsy.
  • Lung biopsy.
  • Breast needle biopsy.
  • Biopsy from known tumor tissue.
  • Suspected malignant lymph nodes, including lymphoma. However, these are generally not urgent when submitted together with a tumor, except mainly for the following (which are generally urgent):

In both these cases, the cases are rushed so that immunohistochemistry can be performed if a metastasis is not readily detected on standard H&E slides, so that it is available by the time the rest of the slides are out. Immunohistochemistry in these cases can detect micrometastases that are not readily visible on H&E stain, but are evident on cytokeratin AE1/AE3. However, if the lab stains such cases regardless of whether H&E stain shows a metastasis or not, then they do not need to be rushed.

Marking cassettes

Use only hard pencil (or specially purchased histology markers), as marks made with pens, Sharpie markers, or scientific freezer-safe markers can get dissolved in tissue processing.[15]

By organ or organ system

Evaluation of tumors

  1. REDIRECT Evaluation of suspected malignancies


  Following are general notes on reporting in pathology.

  • Save your digital work frequently, and also when you leave a desk, even if you think you'll be back shortly. It doesn't matter how much time and effort you spend on something if you're just going to let it disappear.
  • Double-check your report, especially if you copy-pasted and adapted a previous report rather than using a template with blank fields or making your report from scratch.


Selection and trimming

From the stage of selection and trimming, a histopathology report should preferably include:

  • Case:
  • Patient identification and/or sample number
  • Type of tissue sample as described on container
  • Dimensions of original tissue[16]
  • Directions or other features of any inked surfaces.
  • Generally the weight of larger samples[16]
  • Dimensions of pathologic components[16]
  • Whether the entire specimen or representative sections were submitted.

Microscopic evaluation

  • Specimen chronology, often A, B, C, etc., at least where there are multiple specimens from the same case. With multiple specimens, preferably write out the chronology for all of them first, so that you don't miss reporting any of them later.
  • Specimen type and/or surgery type, such as "appendix, appendectomy", for clarification. This is not necessary at all departments.
  • Microscopic description. This is not always necessary, but should be included if the diagnosis is uncertain. One systematic approach is to describe findings from largest to smallest ones. For example, a description of a tumor can start with the demarcation of the tumor, followed by texture, cell shapes, nucleus shapes and chromatin appearance.
  • Diagnosis or most probable diagnoses.
  • If the diagnosis does not clearly account for all conditions that were requested, suspected or asked to be ruled out by the referring clinician (such as stated on the requisition form), you need to classify the specimen as "positive for" versus "negative for" for each such condition, or give a reason for why an evaluation thereof could not be made.
  • In case of malignancy or suspected malignancy:
  • Depth or most distant invasion of malignant findings.[16] Depending on location, it may need to exclude important pathways, such as vascular, neural and/or through capsules or other layers.
  • Whether the resection is radical or not.


Factors supporting a relatively more comprehensive report, particularly in the inclusion of negated findings:

  • Lack of explanation from existing evidence. For example, an inflamed appendix that fits the medical history does not need detailed mention of harmless incidental findings.
  • Prospective review: If your report is likely to undergo double-reading by another pathologist before sign-out, it should either be more detailed, because the doctor who will do the double-reading then gets an idea of your thought process, including what you have looked for versus what may still need to be evaluated. If you know who will do the prospective review for a report of yours, you may alternatively convey your thought process by other means such as directly talking to that person.
  • Highly suspected locations, such as given from the referral.
  • Difficulty in obtaining the specimen, such as a CT-guided biopsy versus a skin shave.
  • Defensive precautions, which appears to be more common among doctors in the Unites States compared to for example Europe.[17][18]

Multiple instances of the same type of pathology (such as lung nodules) can often simply be reported as such, at least with a particular mention of the largest or the most severe example thereof.


Words, from
most likely to
least likely
  • (is)
  • positive for
suspicious for
(benign condition)
cannot be excluded
not likely
(malignant condition)
cannot be excluded
  • negative for
  • effectively ruling out

When something looks very much like a specific entity but you are not sure, preferably use "-like" (or when feasible, "-oid" such as squamoid for squamous-like cells).

When the clinical picture strongly favors a certain condition, and the pathology favors it as well, findings are generally described as "consistent with". Sometimes, "bordering on" can be described when the picture almost fits specified criteria of a specific diagnosis.

It is alright to consider the diagnosis of a pathology report to be a combination of the clinical picture and what can be seen on the specimen. For example, if the microscopy picture is uncertain, you may to a certain degree tend towards the diagnosis that best fits the clinical picture. However, mention differential diagnoses if they are still significantly possible, and would confer a different treatment or another substantially different consequence.

For both findings and diagnoses, is preferable to write "negative for..." rather than "no..." to emphasize the possibility of false negative findings.

Synoptic reports

For cancers, generally include a synoptic report, such as per College of American Pathologists (CAP) protocols at However, synoptic reports are generally not needed for tumor metastases.


Whenever possible, give numerical quantities of sizes, rather than descriptions that are subjective (such as "small" or "large") or variable (such as "apple-sized").


The information contained in the reporting sections in this resource assume that the clinician has requested the exam for the topic at hand, but should still be tailored to any particular questions or requests by the clinician. Any relevant findings beyond the issues or questions raised by the clinician should also be mentioned. The reporting templates in this resource do not cover every recurring situation, so it is often more efficient to create your own repository of report templates that you can copy-paste for various cases. When doing so, however, have marks for relevant items that are frequently changed in the template, which should be readily seen as unfinished in the report if you haven't tailored it to the case at hand (such as "...measuring _____."), so as to avoid omissions or even wrongly entered information from templates.

The most important findings can be moved to near the top of the report if feasible, but doctors performing subsequent double-reading may prefer a consistent anatomic order.


If a certain grammatical rule has a risk of making the report less clear to the reader, ignore that rule in that situation.

Restrict acronyms/abbreviations to those who are certainly well known among all doctors, such as "cm".[notes 7]

Generally describe what can be seen rather than processes (such as preferring "an abundance of" rather than "proliferation of").

If using a dictation device, avoid "no", and instead use "negative for" (and "positive for" in opposite cases), since there's a risk of "no" not being transcribed and thereby creating the opposite meaning.

Skin excisions

In skin cancers, use "peripheral" or "radial" margins (whereas "lateral" margin should be reserved for the margin opposite to the medial margin).[19]


  1. The author has no financial or other conflict of interest in the mentioning of ImmunoQuery.
  2. Do not smear oil on the bottom of the conductor before placing it on a chuck without a specimen, for chuck preparation, as it may (theoretically) cause breakage of the specimen later because of slippage of a segment over the oil layer.
  3. The excision example shows a superficial basal cell carcinoma.
  4. The color of gross specimens generally has very limited clinical significance.
  5. Thicker slices may not become adequately fixated in formalin.
  6. Normal sections from the same tissue helps identifying what is histologically abnormal in the grossly abnormal tissue, versus normal individual variations.
  7. Acronyms/abbreviations increase reading speed only if the reader is familiar with the abbreviated terms:


  1. . Copyrightability of Tables, Charts and Graphs. Deep Blue Repositories, University of Michigan Library. Retrieved on 2022-01-07.
  2. Kräenbring, Jona; Monzon Penza, Tika; Gutmann, Joanna; Muehlich, Susanne; Zolk, Oliver; Wojnowski, Leszek; Maas, Renke; Engelhardt, Stefan; et al. (September 24, 2014). "Accuracy and Completeness of Drug Information in Wikipedia: A Comparison with Standard Textbooks of Pharmacology ". PLOS ONE 9 (9): e106930. doi:10.1371/journal.pone.0106930. PMID 25250889. Bibcode2014PLoSO...9j6930K. 
  3. Ellen D’Hooghe, M.D., Gordan M. Vujanic, M.D., Ph.D.. Kidney tumor - Childhood tumors - Nephroblastoma. Pathology Outlines. Topic Completed: 16 September 2020. Minor changes: 6 October 2021
  4. Shaofeng Yan, M.D., Ph.D.. Skin nonmelanocytic tumor, Carcinoma (nonadnexal), Squamous cell carcinoma. Pathology Outlines. Topic Completed: 13 January 2020. Minor changes: 8 December 2021
  5. A list of included entries and references is found on main image page in Wikimedia Commons: Commons:File:Metastasis sites for common cancers.svg#Summary
  6. There are many variants for the processing of skin excisions. These examples use aspects from the following sources: ". Ochsner J 5 (2): 22–33. 2003. PMID 22826680. PMC: 3399331. Archived from the original. . 
    - With a "standard histologic examination" that, in addition to the lesion, only includes one section from each side along the longest diameter of the specimen.
    - It also shows an example of circular coverage, with equal coverage distance in all four directions.
    - The entire specimen may be submitted if the risk of malignancy is high.
  7. . Breast pathology grossing guidelines. UCLA Health. Retrieved on 2021-09-09.
  8. Katarzyna Lundmark, Krynitz, Ismini Vassilaki, Lena Mölne, Annika Ternesten Bratel. Handläggning av hudprover – provtagningsanvisningar, utskärningsprinciper och snittning (Handling of skin samples - Instructions for sampling, cutting and incision. KVAST (Swedish Society of Pathology). Retrieved on 2019-09-09.
  9. . Paraformaldehyde, Formadehyde and Formalin. Duke University. Retrieved on 2019-12-17.
  10. . Fixation of Tissues. Approval Date: August 2016, August 2020. Review Date: August 2024|website=Royal College of Pathologists of Australia
  11. 11.0 11.1 Buesa RJ, Peshkov MV (2012). "How much formalin is enough to fix tissues? ". Ann Diagn Pathol 16 (3): 202-9. doi:10.1016/j.anndiagpath.2011.12.003. PMID 22483550. Archived from the original. . 
  12. . How to Submit Tissues for Embedding. University of Pittsburgh, Starzl Transplantation Institute. Revised 04/19/21
  13. Monika Roychowdhury. Grossing (histologic sampling) of breast lesions. Topic Completed: 1 August 2012. Revised: 19 September 2019
  14. . Gross Pathology Manual By The University of Chicago Department of Pathology. Updated 2-14-19 NAC.
  15. . Histopathology Services. UNC School of Medicine. Retrieved on 2021-11-15.
  16. 16.0 16.1 16.2 16.3 . An Example of a Melanoma Pathology Report. Melanoma Foundation. Retrieved on 2019-09-24.
  17. Studdert D. M.; Mello M. M.; Sage W. M.; DesRoches C. M.; Peugh J.; Zapert K.; Brennan T. A. (2005). "Defensive medicine among high-risk specialist physicians in a volatile malpractice environment ". JAMA 293 (21): 2609–2617. doi:10.1001/jama.293.21.2609. PMID 15928282. 
  18. Steurer J.; Held U.; Schmidt M.; Gigerenzer G.; Tag B.; Bachmann L. M. (2009). "Legal concerns trigger PSA testing ". Journal of Evaluation in Clinical Practice 15 (2): 390–392. doi:10.1111/j.1365-2753.2008.01024.x. PMID 19335502. 
  19. David Slater, Paul Barrett. Standards and datasets for reporting cancers - Dataset for histopathological reporting of primary cutaneous basal cell carcinoma. The Royal College of Pathologists. February 2019

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