This meta-analysis was performed to evaluate the efficacy and safety profile of moxifloxacin in treatment of urogenital system infections. PubMed, EMBASE, Science Direct, ClinicalTrials.gov, Cochrane Central Register of Controlled Trials, CBM (Chinese Biomedical Literature Database), CNKI (Chinese National Knowledge Infrastructure), Wan Fang Data and VIP INFORMATION were searched from January 1999 to May 2011 to comprehensively collect randomized controlled trials (RCTs) that compared moxifloxacin with conventional antibiotics therapy in patients with urogenital system infections. Clinical cure rates, clinical effective rates, pathogens eradication rates and incidence of adverse drug reactions were pooled using meta-analysis performed by Review Manager 5.1 software. Relative risk (RR) and 95% confidence interval (95% CI) were calculated in a random-effects model or in a fixed-effects model. Twenty-two trials including a total of 3940 patients were included for meta-analysis. The results of meta analysis showed that clinical cure rates, clinical effective rates and pathogens eradication rates of moxifloxacin were higher than conventional therapy [RR = 1.08, 95% CI (1.02, 1.14), P = 0.008; RR = 1.09, 95% CI (1.04, 1.14), P = 0.0005; RR = 1.04, 95% CI (0.99, 1.09), P = 0.08]; the incidences of adverse drug reactions between moxifloxacin and control group were not statistically significant [RR = 0.88, 95% CI (0.72, 1.06), P = 0.17]. In three large studies of pelvic inflammatory disease (PID) patients, no statistically significant difference was found between moxifloxacin monotherapy group and control group about clinical cure rates, microbiological success rates and the incidences of adverse drug reactions [RR = 0.98, 95% CI (0.95, 1.02), P = 0.33; RR = 1.06, 95% CI (0.96, 1.16), P = 0.25; RR = 0.85, 95% CI (0.68, 1.05), P = 0.13]. Moxifloxacin can be suggested as the regimen of choice for treatment of urogenital system infections.