What happens to the lesion after excision? Histopathological examination

Content author: Piotr Rak, MD, PhD, oncological surgeon · Editorial work: Editorial team of Wyspa Medycyny Przyjaznej · Medical review: Piotr Rak, MD, PhD · Date of creation: 07.08.2026 · Date of review: 07.08.2026 · Update: 07.08.2026

The article is educational and describes the general course of histopathological examination. It does not replace discussing a specific result with a doctor - the same description may mean different procedures depending on the clinical situation. The result should not be interpreted independently.

The most important information at a glance

• The excised lesion is sent for histopathological examination - this provides the final diagnosis.
• The material is placed in formalin to stop the decomposition processes and consolidate the tissue structure.
• Fixing, block preparation and staining involve several stages - so the result may not be ready the next day.
• Each type of material is examined: skin biopsy, fine needle biopsy, core needle biopsy and surgical excision.
• These tests are not equivalent, however - they differ in how much tissue they have to evaluate.
• Fine-needle biopsy produces cells, core-needle biopsy produces a fragment of tissue, and excision produces the entire lesion with its surroundings.
• The margin is a layer of healthy tissue excised together with the lesion; it is assessed whether it is free from infiltration.
• The edges of the material are marked with ink so that the pathologist knows where the preparation ends.
• Immunohistochemistry is an additional test used when the image itself is inconclusive.
• Kaszak is also sent for examination - together with the entire capsule, because it determines the recurrence.

Find out more about the specialist

Piotr Rak, MD, PhD, is an oncological surgeon at Wyspa Medycyny Przyjaznej in Gdańsk. Removes skin and subcutaneous lesions and supplies the resulting defects. This text was created from questions asked in the office - and from the belief that a patient who understands what is happening to his material waits more calmly for the result.

Meet Dr. n. med. Piotr Raka

Why is the excised lesion examined at all?

The answer is shorter than patients expect: because only the microscope tells us what this lesion was.

An experienced doctor can assess the lesion with high accuracy based on appearance, interview and dermatoscopy. But assessment is not recognition. A benign lesion may look disturbing, and an early malignant lesion may look quite innocent. The diagnosis is made by a pathologistbased on what he sees in the preparation: what kind of cells they are, how they are arranged, how deep they go, whether they infiltrate the surroundings.

This results in a rule that I repeat at every opportunity: changes of an unknown nature should not be removed using methods that destroy the tissue. Laser, electrocoagulation or freezing do not leave material for examination. The change disappears, and with it the possibility of knowing what it was.

The second reason is equally important and concerns not the lesion itself, but the procedure: the test answers the question whether it was completely removed. More on this in the margin section.

Preparation route - step by step

1. Still in the room: description and marking

Immediately after cutting, the material is placed in a container with fixing fluid, marked with the patient's data and the place of collection. A referral to the laboratory is attached with clinical information - how long the lesion has existed, what it looked like, whether it has changed, and what is suspected.

This is not a formality. The pathologist evaluates the specimen in context, not in a vacuum — the same microscopic image may be interpreted differently depending on where the material comes from and what the history of the change is.

In the case of changes in which spatial orientation is important, the surgeon additionally marks the edges - with a stitch or a description - so that it is known which side of the preparation corresponds to which side of the wound. This is important if it turns out that the cutout needs to be widened: then you know in which direction.

2. Formalin - why choose it?

Tissue deprived of blood supply begins to change almost immediately. The cells disintegrate, the structures become blurred, and after a few hours the preparation would only be suitable for throwing away. The fixer stops this process.

Formalin - or formaldehyde solution - works through protein cross-linking. To put it simply: it stiffens and binds cellular structures together so that the tissue retains the arrangement it had at the time of collection. Thanks to this, what the pathologist sees under the microscope corresponds to reality, and not to the effects of decay.

There are two practical consequences. Firstly, the material must reach the fuser quickly — delay worsens the quality of the preparation. Secondly, the consolidation itself requires time, counted in hours, and longer in the case of larger fragments. This is the first reason why the result cannot be ready the next day.

3. Macroscopic assessment and ink

In the laboratory, the pathologist first examines the material with the naked eye: measures it, describes the appearance of the lesion, its color, boundaries, and distance from the edges.

Then covers the edges of the preparation with special ink. This is a simple and ingenious solution: the ink does not penetrate deep into the tissue, so after cutting the preparation, you can clearly see where the surgical cut surface was. Without this, it would be impossible to distinguish the real edge of the material from an accidental edge created during cutting - and it is at the edge that the margin is assessed.

For larger preparations, inks of several colors are used to distinguish individual pages. Then the material is cut into fragments and placed in cassettes.

4. Paraffin block

The fixed tissue is too soft to be cut into slices several micrometers thick. Therefore, it needs to be hardened - and this is what embedding it in paraffin is for.

First, water is removed from the tissue by passing it through solutions with increasing alcohol concentration, then through an intermediate reagent, and finally it is saturated with paraffin. It's rising paraffin block — ankle in which the tissue is immobilized and protected.

The block has one more advantage that is worth knowing about: it is kept after the study is completed. If, after months or years, you need a consultation with another pathologist or an additional examination, the material still exists and you can return to it. This is why it is worth remembering in which laboratory the test was performed.

5. Cutting and dyeing

The block is cut into slices a few micrometers thick - i.e. thousandths of a millimeter - on a microtome. So thin that the microscope light can pass through it. The sections are placed on slides.

The tissue itself is transparent and colorless, so it must be stained. Basic staining shows cell nuclei in one color and other elements in another - thanks to this, you can see the architecture of the tissue, the shape and size of the nuclei, and the relationship of cells to each other. Most diagnoses are based on this image.

6. Microscopic evaluation and result

The pathologist evaluates the specimen, orders additional tests if necessary, and then formulates a diagnosis and description. The result usually includes the type of lesion, its features, information about margins and - if relevant - additional parameters relevant to further treatment.

Margin - what does it mean and how is it assessed

Margin is a layer of healthy tissue excised together with the lesion. It is not a "just in case" reserve or a sign of an overzealous surgeon. This means that the cells of the lesion can extend beyond its visible border - and the border visible to the naked eye and the microscopic border are two different things.

The margin width is not arbitrary. It depends on what we are removing, where it is located and what the suspicion is. In the case of a benign lesion, it is enough to cut it out within the limits of healthy tissue. In case of a suspected or confirmed malignant lesion, the rules set out in the guidelines - apply and this is one of the reasons why knowledge about the nature of the lesion before the procedure is so important.

What the assessment looks like: the pathologist checks whether the lesion cells are present on the surface marked with ink - i.e. where the cut was made - and how far they reach from this surface.

And one thing I want to make clear, because it is sometimes misunderstood: occupied margin does not mean that the procedure was performed incorrectly. It means that the lesion extended further than the clinical picture indicated - which was impossible to know before the procedure. In such a situation, widening the cutout is a planned element of the procedure, and not a correction of the error. This is why margins are examined.

Immunohistochemistry - when the image alone is not enough

Sometimes the image in basic staining is not conclusive. The cells may look unusual, may resemble several different types of lesions, or may come from a metastatic lesion whose starting point is unknown. Then the pathologist reaches for immunohistochemistry.

The principle of operation is elegant. Antibodies are applied to a piece of tissue that recognize specific proteins present in cells - the ones we are looking for. If a given protein is present, the antibody binds to it, and a color reaction makes the site visible under a microscope. If there is no protein, nothing becomes colored.

This allows us to ask the tissue very specific questions:

• What type of cells is the lesion made of? - Differentiating types that look similar in normal dyeing.
• Where is the change coming from? - when a secondary outbreak is suspected, it helps indicate the probable place of origin.
• What are the characteristics of change? - the presence of specific proteins may be important for treatment planning.
• How do cells actively divide? - Proliferation Index Assessment.

Immunohistochemistry is an additional test performed based on indications, not routinely. It also requires additional time - and this is the most common reason why the result comes later than expected. If this happens, it usually means that the pathologist wants to be sure, not that something has gone wrong.

In selected situations, even more detailed molecular tests are performed - but this is the domain of oncological treatment centers.

Is every material tested the same?

This is one of the most frequently asked questions and the answer is: the principle is the same, but the possibilities are different. Each material goes to the laboratory and is examined under a microscope - but the questions that can be answered depend on how much tissue the pathologist has at his disposal.

The most important takeaway from this table is about margin. No margin biopsy is evaluative — for a simple reason: it takes a fragment of the change, not its boundaries with the environment. Therefore, a biopsy answers the question "what is it?" and an excision additionally answers the question "was it completely removed?" These are two different questions and two different studies.

Second thing: the biopsy result may differ from the result after excision. Not because someone made a mistake, but because the change is heterogeneous - the needle hits one part of it, and the whole may contain areas of a different nature. Therefore, in case of discrepancies, examination of the material from the excision is decisive.

What about semolina?

The question is often asked, usually in the form of: "it's just an ordinary sebaceous cyst, why test it?" I answer: We also send semen for histopathological examination — and that's with the whole bag.

There are two reasons, both practical.

First, confirmation of the diagnosis. A sebaceous lesion - or epidermoid cyst - has a rather characteristic appearance, but it is not the only lesion that looks like this. The same clinical picture may hide other subcutaneous lesions, including those that require completely different treatment. The procedure takes the same amount of time, and the examination concludes the topic definitively.

Secondly - and this is the point - the handbag. A cyst is a cyst: a reservoir surrounded by a wall, filled with content. This wall is active tissue - it is what produces the contents of the cyst. If the contents are removed during the procedure and the sac remains at least in part, the change grows back. Not "sometimes" - it just grows back because the material producing its contents is still there.

Therefore, the aim of the procedure is not to empty the semen, but only enucleation of the entire cyst together with the capsule, preferably in one piece. And that's why this whole preparation - the contents and the bag - goes to the test. The pathologist then confirms the diagnosis and assesses whether the capsule has been completely removed.

Another practical point arises from this. It is best to remove sebaceous cysts when they are not inflamed. When inflamed, the capsule is fragile, fused with the surroundings, and it is much more difficult to remove it completely - and this directly translates into the risk of recurrence. If the lesion is inflamed, the inflammation is usually extinguished first and the procedure is planned later.

Why can't the result be tomorrow

Now that you know the steps, the reason is self-evident. The material must be fixed, described, marked with ink, sectioned, dehydrated, embedded in paraffin, re-sectioned, stained and evaluated. Some of these stages take hours and cannot be sped up without losing the quality of the preparation.

If immunohistochemistry is necessary, another cycle is added. If the pathologist wants to consult the case with another specialist - a few more days. Extended wait times usually indicate care, not a problem.

What is worth determining during the procedure to spend this time more calmly: when to expect the result, how you will receive it and who will discuss it with you. These are three questions worth asking before you leave the office.

And one request: do not interpret the result yourself. The histopathological description is written in a language intended for a doctor, not a patient. The same record may mean completely different procedures depending on age, location, history and what the procedure was like. The search engine does not know this data.

The most common myths

• "The doctor knows by appearance anyway, the examination is a formality." No. The diagnosis is made by a microscope.
• "The lesion can be removed with a laser and sent for examination." No. Methods that destroy tissue do not leave material behind.
• "A busy margin means the surgeon botched the procedure." No. It means that the change went further than was visible.
• "The biopsy assesses whether the lesion has been completely removed." No. The biopsy does not assess the margin.
• "The biopsy result always agrees with the resection result." Not always - changes may be heterogeneous.
• "Kaszaka does not need to be examined." You need it - and with the whole bag.
• "Just squeeze out the contents of the casserole." No. A capsule left behind indicates a recurrence.
• "A long wait for the result is a bad sign." Usually means additional tests or consultation.
• "The preparation is discarded after the test." No. The blocks and slides are stored and can be accessed again.

Do you have a change to remove or a result to discuss?

We send each removed lesion for histopathological examination - including sebaceous cyst. We discuss the result in person, explaining what it means for further action.

Removal of lesions at the Friendly Medicine Island in Gdańsk

At the Friendly Medicine Island, we remove skin and subcutaneous lesions surgically, with a planned margin and dressing the resulting defect. We send the material for histopathological examination and discuss the results with the patient - along with information about the results and whether further steps are needed.

This also applies to lesions considered "ordinary", such as atheroma or lipoma. The procedure takes the same amount of time, and the examination concludes the matter without any understatements. The current scope of treatments, availability of dates and prices should be confirmed during registration.

Contact us Price list

What to ask during the treatment?

• Will the lesion be sent for histopathological examination?
• What margin is planned and why?
• When will the result be ready?
• How will I receive it and who will discuss it with me?
• What happens if the margins are not free?
• May additional tests be needed, e.g. immunohistochemistry?
• In which laboratory is the test performed?
• Will the material be kept for consultation?
• Would a biopsy instead of excision be sufficient for this lesion?
• What will the wound and scar look like?
• Will I need a follow-up after the result?
• What should I worry about during healing?

FAQ - histopathological examination

What happens to the lesion after excision?

It goes to a container with a fixative and to the laboratory, where it is described, marked with ink, cut, embedded in paraffin, cut again into thin sections, stained and assessed under a microscope by a pathologist.

Why is the material placed in formalin?

Tissue deprived of blood supply disintegrates quickly. Formalin stops this process by cross-linking proteins and fixing the tissue structure in its state at the time of collection. Without this, the preparation would not be suitable for evaluation.

What is histopathological examination?

This is an assessment of the tissue under a microscope, giving a final diagnosis - what kind of cells they are, how they are arranged, how deep they go and whether they infiltrate the surroundings. No imaging test or clinical evaluation replaces it.

What is margin?

This is a layer of healthy tissue excised together with the lesion because the cells can extend beyond the visible border. The pathologist assesses whether lesion cells are present on the edges of the specimen.

Why is the preparation marked with ink?

Ink marks the surface of the surgical cut. Thanks to it, after cutting the preparation, you can see where the real edge of the material was - and this is where the margin is assessed.

What does "margin busy" mean?

That the cells of the lesion are present on the cutting surface, which usually means that the excision needs to be widened. This is not a surgeon's error - the lesion extended further than the image before the procedure indicated.

What is immunohistochemistry?

An additional test in which antibodies recognizing specific proteins in cells are applied to the section. The color reaction shows whether a particular protein is present - which helps determine the type of lesion, its origin and characteristics important for treatment.

Are biopsy and excision examined the same?

The principle is the same, but the possibilities are different. Fine-needle biopsy yields cells, core biopsy and skin biopsy yield a fragment of tissue, and surgical excision yields the entire lesion and its surroundings. Only the latter allows you to assess the margin.

Can the biopsy result differ from the result after excision?

Maybe, because the changes are heterogeneous - the needle hits one part, and the whole may contain areas of a different nature. In case of discrepancies, examination of the material from the cutout shall be decisive.

Is semen sent for testing?

Yes - including the whole bag. The examination confirms the diagnosis and allows you to assess whether the cyst has been completely removed. Other subcutaneous lesions may hide behind the image of "ordinary sebaceous cyst".

Why does semen grow back?

Because a piece of the bag was left behind. It is the wall of the cyst that produces its contents - simply emptying the lesion does not solve the problem. The aim of the procedure is to remove the entire cyst and its capsule.

Why does it take so long to get the result?

Because the subsequent stages - fixing, dehydration, embedding in paraffin, cutting and staining - take time and cannot be accelerated without losing quality. Additional tests or consultations extend this time, usually indicating care rather than a problem.

Sources

• Island of Friendly Medicine, contact: https://www.wyspamedycynypowiedzaznej.pl/pl/kontakt
• NHS, Biopsy: https://www.nhs.uk/conditions/biopsy/
• NHS, Skin biopsy: https://www.nhs.uk/conditions/skin-biopsy/
• NHS, Skin cyst: https://www.nhs.uk/conditions/skin-cyst/
• NHS, Lipoma: https://www.nhs.uk/conditions/lipoma/
• NHS, Melanoma skin cancer: https://www.nhs.uk/conditions/melanoma-skin-cancer/
• NHS, Non-melanoma skin cancer: https://www.nhs.uk/conditions/non-melanoma-skin-cancer/
• DermNet, Skin biopsy: https://dermnetnz.org/topics/skin-biopsy
• DermNet, Histology of the skin: https://dermnetnz.org/topics/histology-of-the-skin
• DermNet, Immunohistochemistry: https://dermnetnz.org/topics/immunohistochemistry
• DermNet, Epidermoid cyst: https://dermnetnz.org/topics/epidermoid-cyst
• DermNet, Skin surgery: https://dermnetnz.org/topics/skin-surgery
• NICE, Melanoma: assessment and management (NG14): https://www.nice.org.uk/guidance/ng14
• Royal College of Pathologists, information for patients: https://www.rcpath.org/discover-pathology.html