OBJECTIVES: Pouchitis is the most frequent long-term complication of ileal pouch-anal anastomosies (IPAA) surgery for ulcerative colitis (UC) which is a nonspecific inflammation of the ileal reservoir. Its clinical frequency varies depending on the definition and the follow up but is approximately 50% after a decade. Antibiotics and probiotics are currently the most widely accepted treatment in pouchitis patients. Objective of this study was to meta-analyze efficacy of probiotics and antibiotics in the management of pouchitis. METHODS: All databases specially Pubmed, Web of Science, Scopus, Cochrane, and Google Scholar were searched between 1965 and December 2009, and relevant controlled clinical trials were extracted, reviewed, and validated according to the study protocol. The outcome of interest was defined by a pouchitis disease activity index (PDAI)<7. Thirteen clinical trials were included in the meta-analysis. RESULTS: Pooling of the results from eight trials yielded a relative risk (RR) of 5.33 with a 95% CI of 2.12-13.35 and a significant RR (P= 0.0004) in the treatment group in comparison with the placebo group. Summary RR for clinical improvement in 6 trials was 14.17 with a 95% CI of 1.19-168.93 (P= 0.036) in efficacy of VSL#3 (all doses) comparing to placebo and slightly more effective for VSL#3 (6 g/day) comparing to placebo with RR of 20.35 with a 95% CI of 6.16-67.22 (P<0.0001). Efficacy of antibiotics comparing to placebo showed a summary RR of 2.68 with a 95% CI of 0.4-17.99 and P= 0.3107 for clinical improvement in three trials. The summary RR for efficacy of ciprofloxacin comparing to metronidazole was 0.68 with a 95% CI of 0.44-1.06 (P= 0.8913). CONCLUSIONS: In conclusion, alongside the benefit of probiotics and antibiotics in the management of pouchitis, effects of probiotics and antibiotics on pouchitis vary according to different mixtures of microorganisms strains in probiotics and different spectrums of antibiotics.