“Skip Lesions” and Transmural Inflammation: What Those Pathology Terms Mean in Crohn’s
Last Updated Jan 15, 2026
Pathology reports for Crohn’s disease often include short phrases that sound intimidating. Terms like skip lesions and transmural inflammation are not diagnoses by themselves. They are descriptive “Crohn’s pathology terms” that help explain what the inflammation looks like, where it is, and how deep it may go. Understanding these words can make the results feel less mysterious and can clarify why a care team might also use endoscopy reports, imaging, and symptoms together when talking about risk and next steps.
Skip lesions and patchy colitis: the “patchy” pattern in Crohn’s
People searching “skip lesions Crohn’s meaning” are usually trying to decode the idea that inflammation can appear in an on-and-off pattern. In Crohn’s disease, inflamed areas can be separated by stretches of tissue that look more normal. This is what “skip lesions” describes, a patchwork pattern rather than one unbroken segment.
When Crohn’s affects the large intestine (colon), a report may use phrases like patchy colitis (Crohn’s) or “focal” inflammation. This points to the same general idea: inflammation is not evenly spread throughout the colon. On colonoscopy, this can look like discrete ulcers with normal-looking mucosa (lining) between them, rather than continuous inflammation starting at the rectum and moving upward. Pathology can echo this by describing inflammation that is “highly focal” or “segmental,” and some reports may note that the rectum is relatively spared. These patterns can support Crohn’s disease in the bigger diagnostic picture, especially when combined with symptoms and imaging findings. [1]
Transmural inflammation, cobblestoning, and granulomas: what they suggest about depth and complications
Transmural inflammation meaning: inflammation that can extend through the full thickness of the bowel wall, not only the surface lining. This matters because deeper inflammation can help explain why Crohn’s is linked with certain complications over time. For example, bowel wall thickening and scarring can contribute to narrowing that may lead to obstruction, and ulcers can sometimes extend through the intestinal wall and form fistulas (abnormal connections). [2]
Two other common Crohn’s pathology terms are tied to this deeper, uneven inflammation pattern:
Cobblestoning (Crohn’s): a “cobblestone” look of the lining that can happen when swollen tissue and deeper ulcers create a bumpy surface pattern.
Granulomas (Crohn’s): small clusters of immune cells (often called noncaseating granulomas) that may appear on biopsy in some people, but not everyone.
A classic description in Crohn’s is cobblestoning with skip areas of disease, and some sources note granulomas occur in a minority of patients, so their absence does not rule Crohn’s out. [3]
When a report mentions granulomas, clinicians often treat it as a supportive clue, especially alongside other Crohn-like features. European Crohn’s and Colitis Organisation (ECCO) guidance notes that granulomas plus at least one other feature can help establish Crohn’s disease, but also emphasizes that finding a granuloma is not always necessary for diagnosis. [4]