The objective of this study was to evaluate and collect current evidence on the effect of probiotics in preventing pouchitis after restorative ileal pouch anal anastomosis (IPAA). The Pubmed, Medline, EMbase, CINAHL, Web of Science, and Scopus bibliographic, and Google Scholar databases were searched between 1966 and May 2007, and relevant controlled clinical trials were extracted, reviewed, and validated according to the study protocol. The outcome of interest was for pouchitis defined by a pouchitis disease activity index (PDAI) > or =7. Five randomized, placebo-controlled clinical trials were included in the meta-analysis. Pooling of the results from these trials yielded an odds ratio (OR) of 0.04 with a 95% CI of 0.01-0.14 (P < 0.0001) in the treatment group in comparison with the placebo group. In conclusion, the benefit of probiotics in the management of pouchitis after IPAA operation was confirmed by the meta-analysis.