Reading Your Pathology Report

Pathology reports from colonoscopy or endoscopy biopsies can look very technical. They use specific words to describe what the pathologist saw under the microscope. Learning what a few key terms mean, especially chronicity, granulomas, and dysplasia, can help people with inflammatory bowel disease (IBD) understand how biopsies support diagnosis and cancer surveillance. This article explains these terms in plain language and how they fit into IBD care.

Key takeaways

• A pathology report is a microscope description of biopsy tissue, not a full diagnosis by itself.

• Chronicity describes long-standing inflammation and helps distinguish IBD from short-term infections.

• Granulomas are special clusters of immune cells that can support a diagnosis of Crohn’s disease.

• Dysplasia means precancerous change in the lining cells and is key for colon cancer surveillance in IBD.

• Any result that mentions dysplasia, granulomas, or “indefinite” findings should be reviewed with the IBD care team.

How to think about a pathology report

A pathology report describes what the pathologist sees when biopsy tissue is examined under the microscope. For IBD, these biopsies often come from the colon, rectum, or small intestine.

Most reports are organized into sections such as:

• Specimen: Where the tissue came from, for example “terminal ileum,” “ascending colon,” or “rectum.”

• Gross description: How the tissue looked to the naked eye.

• Microscopic description: Detailed features seen under the microscope.

• Diagnosis or final diagnosis: A summary phrase, such as “chronic active colitis, consistent with IBD.”

• Comment: Extra explanation about possible causes or clinical relevance.

For IBD, the report is combined with symptoms, endoscopy images, lab results, and imaging. Diagnosis almost never relies on pathology alone.

“Chronicity” – signs of long-standing inflammation

Chronicity describes changes that suggest inflammation has been present for a long time, not just a sudden short infection.

Pathologists look for several chronic features in the colon or small bowel:

• Architectural distortion: The normal test-tube like glands (crypts) of the intestine become irregular, branched, or widely spaced.

• Basal plasmacytosis: Clusters of immune cells called plasma cells collect at the base of the glands near the muscular wall.

• Paneth cell metaplasia in the left colon: A type of cell usually seen in the small intestine appears lower down in the colon.

• Chronic inflammatory cells in the lining and deeper wall.

A report might use phrases such as:

• “Chronic colitis”

• “Features of chronicity present”

• “Chronic active colitis”

This matters because:

• Chronic changes support IBD over a one-time infection like food poisoning.

• Lack of chronicity with only short-term changes may suggest an acute infection, ischemia (low blood flow), or drug injury.

“Chronic active colitis” usually means both long-standing changes and recent active inflammation such as cryptitis (neutrophils inside the glands) or crypt abscesses.

Granulomas – when they point toward Crohn’s disease

A granuloma is a small organized collection of immune cells, especially macrophages and epithelioid cells, that form a tight cluster. In IBD pathology, the most important type is a noncaseating granuloma, which has no cheesy necrosis in the center.

Granulomas can have different meanings:

• Granulomas away from areas of obvious ulcer or crypt rupture are more typical of Crohn’s disease.

• Granulomas that sit right on a damaged crypt or fissure may be a reaction to local injury and are less specific.

• Certain infections (such as tuberculosis or some fungal infections) can also cause granulomas, often with special staining or culture clues.

A report may say:

• “Noncaseating granulomas identified, suggestive of Crohn’s disease in the right clinical setting.”

• “Poorly formed granulomas, could reflect chronic injury or infection. Correlate clinically.”

Why granulomas matter:

• When present in the right location and after infections are ruled out, they support Crohn’s disease rather than ulcerative colitis.

• Many people with Crohn’s disease never have granulomas found, because granulomas can be patchy or missed in small biopsy samples.

• Granulomas alone do not confirm Crohn’s disease. The care team still combines this with scope findings and imaging.

Dysplasia – precancerous change in IBD

Dysplasia means abnormal growth and appearance of the cells that line the colon or rectum. It is considered precancerous, which means it can progress to colorectal cancer over time if not managed.

For people with long-standing ulcerative colitis or extensive Crohn’s colitis, regular colonoscopies with biopsies are used to watch for dysplasia as part of cancer surveillance.

Pathologists usually classify dysplasia as:

• Negative for dysplasia: No precancerous change seen. Inflammation may still be present.

• Indefinite for dysplasia: Worrisome changes, but active inflammation or poor sample quality makes it hard to be sure.

• Low-grade dysplasia (LGD): Definite precancerous changes, but still early and more organized.

• High-grade dysplasia (HGD): More serious abnormalities and a higher risk of nearby cancer.

Reports may also distinguish between:

• Polypoid or visible dysplasia: Localized in a polyp or raised lesion that can sometimes be removed completely.

• Flat or invisible dysplasia: Found only on random biopsies from apparently normal-looking tissue.

Why dysplasia findings are so important:

• Low-grade dysplasia in IBD needs careful review. Management might involve closer surveillance or removal of the affected area, depending on whether it can be completely resected.

• High-grade dysplasia often leads to strong consideration of surgery to remove the colon, because cancer risk is higher and cancer may already be nearby.

• “Indefinite for dysplasia” usually leads to repeat colonoscopy after inflammation is better controlled so the pathologist can get a clearer look.

The exact plan depends on the extent of disease, whether the dysplasia is visible and completely removed, and personal risk factors such as primary sclerosing cholangitis or family history of colorectal cancer.

Other common phrases on IBD biopsy reports

Although this article focuses on chronicity, granulomas, and dysplasia, several other phrases often appear:

• Active colitis or active ileitis: Neutrophils are present, showing current inflammation.

• Quiescent colitis: Chronic changes are present but no active inflammation.

• Crypt abscesses: Neutrophils filling the glands, a sign of active inflammation.

• Erosions or ulcers: Breaks in the surface lining.

• Consistent with IBD / suggestive of IBD: Microscopic findings match IBD but are not absolutely specific.

• Nonspecific colitis: Inflammation that does not clearly fit IBD, infection, or another single cause.

These phrases help the care team judge how active the disease is and whether current treatment is effective.

Putting it together with the care team

A pathology report is one piece of the overall IBD picture. It cannot answer questions like “Is this person in full remission?” or “Which medication is best?” on its own.

Helpful questions for a visit with a gastroenterologist or IBD nurse might include:

• Does the report show chronicity, and what does that mean for the diagnosis?

• Were any granulomas found, and do they support Crohn’s disease?

• Is there any mention of dysplasia, “indefinite,” or “atypia”?

• Do the biopsy results match the endoscopy pictures and current symptoms?

• Will these findings change surveillance intervals or treatment goals?

Understanding these key terms can make it easier for people with IBD and their families to follow conversations about diagnosis, disease activity, and long-term cancer prevention.

FAQs

Does “chronic colitis” on a biopsy mean definite IBD?

“Chronic colitis” means the pathologist sees long-standing inflammation in the colon. This strongly raises concern for IBD, especially when symptoms and scope findings match. However, other less common conditions can sometimes cause chronic-looking changes. Diagnosis still depends on the full clinical picture.

If there are no granulomas, can Crohn’s disease be ruled out?

No. Many confirmed Crohn’s cases never show granulomas on biopsy, even after years. Granulomas support Crohn’s when present in the right pattern, but their absence does not rule it out.

Is dysplasia the same as cancer?

No. Dysplasia is precancerous, not invasive cancer. It shows that cells are on a pathway that could become cancer if left alone. The grade of dysplasia and whether it can be removed safely guide next steps, which can range from closer surveillance to surgery.

What does “indefinite for dysplasia” actually mean?

“Indefinite for dysplasia” means the pathologist sees some worrisome changes, but active inflammation, poor orientation, or other factors make it impossible to call it clearly negative or positive. The usual response is to improve inflammation control and repeat colonoscopy with careful biopsies.