Abstract Background For patients with inflammatory bowel disease (IBD), surgical intervention is sometimes required due to medically refractory colitis or development of neoplasia. Restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) is the most common procedure for patients with colitis. However, pouchitis can develop in up to 80% of patients after the surgery and significantly impairs quality of life. Despite the high prevalence of pouchitis, endoscopic phenotypes have not been clarified. This study assessed the frequency and characteristics of inflammation involving the rectal cuff. Methods This is a retrospective study from a tertiary IBD center of IBD patients treated by total proctocolectomy with IPAA and subsequently underwent pouchoscopies at the University of Chicago between January 2007 and September 2019. We reviewed the endoscopic findings in different areas of the pouch: the pre-pouch ileum, inlet, “tip of the J”, proximal and distal pouch, anastomosis, rectal cuff, anal canal, and perianal area. This analysis evaluated all available pouchoscopies per patient and included patients with normal cuff and those with cuffitis noted in every pouchoscopy. Demographic and endoscopic data were assessed to compare patients with normal cuff and those with cuffitis. Fisher’s test was used for a univariate analysis to assess factors contributing to cuffitis. Logistic regression analysis was performed as a multivariate analysis including univariate variables with a P-value < 0.15. Results We reviewed 1,081 pouchoscopies from 426 IBD patients who underwent proctocolectomy with IPAA and identified 184 patients (43%) with normal cuff and 107 (25%) with cuffitis. Of these 291 patients, 57% were men, 92% were Caucasian, the mean age at the diagnosis (SD) was 26 ± 12 years, and mean BMI 26 ± 5 kg/m2. The diagnosis before surgery for these patients were for ulcerative colitis (91%), indeterminate colitis (5.8%), and Crohn’s disease (1.7%). A significant difference (P = 0.003) was found in the frequency of pouchitis between patients with normal cuff (126/184, 69%) and those with cuffitis (90/107, 84%) (Table 1). Although not statistically significant, the frequency of pouch failure in patients with cuffitis (13/107, 12%) was higher than those with normal cuff (12/184, 6.5%). Multivariate analysis showed pouchitis was significantly associated with cuffitis (OR = 2.2; 95% CI = 1.2–4.2; P = 0.01) (Table 2). Endoscopic data showed that the pre-pouch ileum was significantly (P = 0.001) involved in patients with cuffitis (45/90, 50%) compared with those with normal cuff (36/126, 29%). Conclusion Our analysis of 291 patients suggested that cuff inflammation can be a significant risk factor of pouchitis and is significantly associated with the development of inflammation in the pre-pouch ileum. Cuffitis can be a therapeutic target to improve J pouch outcomes.