Probiotics have been used for the treatment of inflammatory bowel diseases (IBD). However, the effects of probiotics on the induction and maintenance of remission in ulcerative colitis (UC) or Crohn's disease (CD) still remain controversial. This systematic review verified the findings of high-quality randomized controlled trials (RCTs) which investigated the therapeutic effects of probiotics on IBD. After the quality assessment, 20 RCTs which investigated the effects of probiotics on the induction or maintenance of remission in IBD were identified. From the results of the validation of these RCTs, beneficial effects of probiotic treatments to improve the response rate and remission rate on the remission induction therapies [risk ratio (RR) 1.81; 95 % confidence interval (CI) 1.40-2.35 and RR 1.56; 95 % CI 0.95-2.56, respectively] were verified. Furthermore, probiotic treatments exhibited effects equal to mesalazine on the maintenance of remission in UC (RR 1.00; 95 % CI 0.79-1.26). In contrast, no significant effect of probiotic treatments was shown in either the induction or maintenance of remission in CD. Because there were many variations in the conditions among these studies, a further analysis evaluating the effects of probiotic treatments in IBD is needed to clarify the optimal probiotics and treatment regimens for each condition or population in IBD patients.