Aliment Pharmacol Ther 31 , 862–873 Summary Background Diagnosis and management of chronic antibiotic‐refractory pouchitis and Crohn’s disease of the pouch can be challenging. Pyloric gland metaplasia is a histological feature indicative of chronic mucosal inflammation. Its value in diagnosis and prognosis of pouch disorders has not been investigated. Aim To assess the prevalence, diagnostic and prognostic value, and risk factors of pyloric gland metaplasia in pouch patients. Methods Patients were identified from our prospectively maintained Pouchitis Database. Pouch biopsy specimens were re‐reviewed for pyloric gland metaplasia and other histological features. Two cohorts of patients were studied: a historical cohort ( n = 111) and the second, a validation cohort ( n = 100). Univariate and multivariate analyses were performed to assess risk factors for pyloric gland metaplasia. Results The prevalence of pyloric gland metaplasia in the historical cohort and validation cohort was 45 (40.1%) and 24 (24.0%), respectively. The sensitivity and specificity of pyloric gland metaplasia for the diagnosis of chronic antibiotic‐refractory pouchitis or Crohn’s disease were 70.7% and 92.5%, respectively, for the first cohort and 39.0% and 86.4%, respectively, for the 2 nd validation cohort. In multivariate analysis of the first cohort, patients with refractory pouchitis or Crohn’s disease were 28 times (95% CI, 7.3–107.1) more likely to have pyloric gland metaplasia than those with a normal pouch or irritable pouch syndrome. The factor of refractory pouchitis or Crohn’s disease remained in the model for the 2 nd validation cohort with odds ratio of 4.58 (95% CI, 1.6–13.4). Conclusions Pyloric gland metaplasia is associated with diagnosis of chronic antibiotic‐refractory pouchitis or Crohn’s disease of the pouch and appears to be a specific marker for both disease entities.