Abstract Background Ulcerative colitis (UC) patients who undergo ileal pouch-anal anastomosis (IPAA) without mucosectomy may develop inflammation of the rectal cuff (cuffitis). Studies have suggested that cuffitis is associated with clinical pouch inflammation (pouchitis), but it remains unclear if cuffitis is associated with specific endoscopic phenotypes of pre-pouch inflammation (ileitis), pouch body inflammation, and diffuse pouch inflammation. Therefore, this aim of this study is to identify if endoscopic cuffitis is a predictor of more severe pouch phenotypes, which may warrant earlier or more aggressive treatment. Methods In this cohort study, charts were reviewed of patients who underwent IPAA at a tertiary care center from 01/2010 to 12/2021. Inclusion criteria for this study were a diagnosis of UC and ≥18 years old at time of colectomy. Exclusion criteria were lack of endoscopic evaluations after the peri-operative period (defined as 6 months following ileostomy closure) and diagnoses other than UC requiring IPAA. Patients were divided into cohorts based on whether they had cuffitis identified on ≥1 endoscopy following IPAA, which was confirmed by two researchers. Outcomes for this study included pre-pouch ileitis, pouch body inflammation, and diffuse inflammation (inflammation of the pouch body, inlet, and pre-pouch ileum). A multivariate logistic regression was used to test for association between cuffitis and each outcome while controlling for potentially confounding variables suggested to be significant on univariate analyses. Results A total of 363 patients were included in this study with an overall median follow-up time of 2.4 (IQR 1.2-3.8) years after ileostomy closure. 149 (41.0%) patients had cuffitis on ≥1 endoscopy following IPAA. 65 (17.9%) patients developed pre-pouch ileitis (Table 1), which was significantly associated with cuffitis (aOR = 3.85; 95% CI 2.15-6.91; p < 0.0001) and age (aOR = 0.98, 95% CI = 0.96-1.00, p = 0.0254). Pouch body inflammation occurred in 201 (55.4%) patients and was associated with cuffitis (aOR = 2.69, 95% CI = 1.69-4.29, p < 0.0001), PSC (aOR = 6.60, 95% CI = 1.85-23.49, p = 0.0036), extraintestinal manifestations (EIMs) other than PSC (aOR = 2.35, 95% CI = 1.45-3.79, p = 0.0005), and age (aOR = 0.98, 95% CI = 0.97-1.00, p = 0.0359). Finally, diffuse inflammation occurred in 20 (5.5%) patients and was associated with cuffitis (aOR = 6.24, 95% CI = 2.04-19.08, p = 0.0013). Conclusion Endoscopic cuffitis is associated with the development of severe inflammatory pouch phenotypes. Future studies are needed to investigate whether treatment of cuffitis reduces this risk and whether the incidence of cuffitis is rising similar to pouchitis in the post-biologic era.