The fate of the excluded rectal segment after surgery for Crohn's colitis remains poorly defined. To determine prognostic factors relating to the fate of the rectal segment, records of 47 patients who underwent creation of an excluded rectal segment were studied. Disease developed in 33 patients (70 percent) in the excluded rectal segment by five years; 24 patients (51 percent) had completion proctectomy by 2.4 years; and 9 patients (19 percent) retained a rectum with disease at a median follow-up period of five years (range, 2-13 years). At a median follow-up time of six years (range, 2-21 years), 14 patients were without clinical disease. The three groups were equivalent with respect to sex, duration of preoperative disease, indication for operation, distribution of disease, and histologic involvement of the proximal rectal margin. The median age of patients in the proctectomy group at diagnosis tended to be younger than that of patients with a retained excluded rectal segment (22, 30, and 31 years for patients having proctectomy, patients with a diseased excluded rectal segment, and patients with a normal excluded rectal segment, respectively). Neither initial involvement of the terminal ileum nor endoscopic inflammatory changes seen in the rectum predicted eventual disease of the excluded rectal segment. However, initial perianal disease complicating Crohn's colitis was predictive of persistent excluded rectal segment disease and often required proctectomy. Therefore, because the presence of perianal disease and Crohn's colitis predicts persistent or recurrent excluded rectal segment disease, primary total proctocolectomy or early completion proctectomy may be indicated in this subgroup of patients.