PURPOSE: Inflammation occurs in defunctioned rectums in patients without inflammatory bowel disease. Defunctioned rectums in patients with inflammatory bowel disease have additional histopathologic changes that can cause diagnostic confusion. The aim of this study was to ascertain whether histologic changes in defunctioned rectums had any association with original pathologic diagnosis in the colectomy specimen, duration of defunctionalization, or occurrence of Crohn's disease-like complications during follow-up. METHODS: In this retrospective study, we reviewed the patient records and reexamined histologically the defunctioned rectums and original colectomy specimens of 84 consecutive patients encountered between 1983 and 1986. RESULTS: All excised rectal specimens had ulcers and erosions, usually with prominent mucosal lymphoid aggregates, often with mucosal atrophy, diffuse mucin depletion, and marked mucosal architectural distortion. Transmural lymphoid aggregates were identified in 56 patients (67 percent) and were graded as moderate or marked in 35 (42 percent). Ten rectal specimens contained nonnecrotizing granulomas. The original pathologic diagnoses from the colectomy specimens were as follows: ulcerative colitis (n = 22), Crohn's disease (n = 19), indeterminate colitis (n = 41), adenocarcinoma (n = 1), and diverticular disease (n = 1). Only mild histologic changes were observed in rectal specimens from patients with diverticular disease and adenocarcinoma, and granulomas were identified more frequently in Crohn's disease patients. Otherwise, no feature in the defunctioned rectum was associated with the original diagnosis or duration of defunctionalization. Sixteen patients (19 percent) had late surgical complications suggestive of Crohn's disease (abscess, fistula, or subsequent biopsy specimen containing nonnecrotizing granulomas) after a median follow-up of 4.8 years. Five were patients categorized as having Crohn's disease with colectomy specimen, nine had indeterminate colitis, and two had ulcerative colitis. No histologic feature in the defunctioned rectum was associated with Crohn's disease-like complications. CONCLUSIONS: Granulomas in a defunctioned rectum were associated with an original diagnosis of Crohn's disease. Transmural lymphoid aggregates were common in defunctioned rectums in patients with inflammatory bowel disease and did not indicate Crohn's disease. Other histologic changes developed independently of diagnosis and duration of defunctionalization.