Background: Pouchitis is the most common complication of proctocolectomy with ileo-pouch-anal anastomosis (IPAA) for ulcerative colitis (UC). No previous study in Mexico has evaluated this issue; our aim was to evaluate its frequency, clinical characteristics and factors associated with its presence in Mexican patients with UC and IPAA. Methods: Retrospective-cohort study including 70 patients with histopathological diagnosis of UC and IPAA between 1983 and 2014 from inflammatory bowel disease clinic of a tertiary care center. The statistical analysis used descriptive statistics, chi-square and Fisher's exact test for categorical variables and Student's t test for numeric variables. Univariate analysis was performed to identify the factors associated. Results: Patients presenting with pouchitis accounted for 48.6%. From the 34 cases, 12 (35.3%) had inactive pouchitis; 7 (20.6%) active acute pouchitis; 15 (44.1%) chronic active pouchitis. On average, pouchitis occurred 5.37 years after IPPA. Factors probably associated with its occurrence were the presence of autoimmune concomitant diseases (ACDs; p = 0.06, OR 4.40, 95% CI 0.84-22.9) and extra-intestinal manifestations (EIMs; p = 0.05, OR 2.53, 95% CI 0.96-6.64), which was also probably associated with chronic active pouchitis (p = 0.06, OR 0.31, 95% CI 0.07-1.31). Conclusions: The frequency of pouchitis is high in Mexican UC patients after IPAA. ACDs and EIMs were probably associated with its development.