Objective To compare the clinical therapeutic effect of probiotic agents in treating irritable bowel syndrome (IBS) by Meta-analysis. Methods Such databases as MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials, and Chinese Biomedical Literature Database were searched from January 2001 to October 2011, and the domestic conference proceedings and relevant papers published in recent 1 year were also searched manually. All domestic randomized controlled trials (RCTs) on probiotic agents in treating irritable bowel syndrome (IBS) were collected, which were then selected according to the inclusion and exclusion criteria. The data were extracted, the methodological quality of the included studies was assessed, and the Meta-analysis was performed with Revman5.0. Results A total of 11 RCTs involving 1 065 patients were included. The total effective rate of the probiotic agents plus conventional treatment group was superior to that of the conventional treatment (trimebutine meleate/ pinaverium bromide) group (RR=1.26, 95%CI 1.18 to 1.34, Plt;0.000 01), it could effectively relieve abdominal pain (RR=1.10, 95%CI 1.03 to 1.18, P=0.004) and diarrhea (RR=1.15, 95%CI 1.07 to 1.24, P=0.000 3). But there was no significant difference between the two groups in alleviating abdominal distention (RR=1.08, 95%CI 0.95 to 1.24, P=0.25). The effectiveness of probiotic agents used alone was similar to that of the conventional treatment used alone, without significant differences (RR=0.85, 95%CI 0.66 to 1.09, P=0.19). Conclusion Probiotic agents combined with conventional drugs can improve the total therapeutic effect of IBS, especially in alleviating abdominal pain, diarrhea and so on. But the effectiveness of probiotic agents used alone is similar to that of the conventional treatment used alone. For the possibility of bias due to the lower quality of the included studies and unclear implementation of RCTs, this conclusion should be verified with more large-scale and high-quality RCTs.