Purpose of review One of the significant limitations to the investigation of inflammatory bowel disease (IBD) in humans is the impossibility of studying this condition from the beginning of the disease process to understand the individual contribution of the various microbiological and immunological components to its pathogenesis. Pouchitis can serve as a human model for IBD, as the time of the pouch creation is known, which allows to prospectively study the events that might eventually lead to the development of a form of intestinal inflammation (i.e., pouchitis) that mimics IBD. Recent findings A considerable amount of progress has been made in the last few years on the mechanisms underlying the pathogenesis of pouchitis. Recent literature suggests that pouchitis may present a spectrum of disease processes, with a wide range of causes, risk factors, clinical phenotypes, disease courses, and prognoses. Genetic, microbiological, and immunological profiles in pouchitis were evaluated. Summary Ileal pouch and pouchitis represent a valuable human model to study the evolution of bacterial communities and host-bacteria interactions in IBD by sequentially monitoring microbiological and immunological profile before, during, and after pouch construction and before and after development and treatment of pouchitis.