BACKGROUND: Men who have sex with men (MSM) are a high risk population for human immunodeficiency virus (HIV) infection. Our study aims to find whether MSM who were recruited online had a higher prevalence of self-reported unprotected anal intercourse (UAI) than those who were recruited offline. METHODS: A meta-analysis was conducted from the results of published studies. The analysis was stratified by the participants' geographic location, the sample size and the date of the last reported UAI. RESULTS: Based on fourteen studies, MSM who were recruited online (online-based group) reported that 33.9% (5,961/17,580) of them had UAI versus 24.9% (2,700/10,853) of MSM who were recruited offline (offline-based group). The results showed that it is more likely for an online-based MSM group to have UAI with male partners than an offline-based MSM group [odds ratio (OR) = 1.35, 95% CI = 1.13-1.62, P < 0.01]. The subgroup analysis results also showed that the prevalence of UAI was higher in the European subsample (OR = 1.38, 95% CI = 1.17-1.63, P < 0.01) and in sample sizes of more than 500 individuals (OR = 1.32, 95% CI = 1.09-1.61, P < 0.01) in the online group compared to the offline group. The prevalence of UAI was also significantly higher when the time of the last UAI was during the last 3 or more months (OR = 1.40, 95% CI = 1.13-1.74, P < 0.05) in the online group compared to the offline group. A sensitivity analysis was used to test the reliability of the results, and it reported that the results remained unchanged and had the same estimates after deleting any one of the included studies. CONCLUSIONS: A substantial percentage of MSM were recruited online, and they were more inclined to engage in UAI than MSM who were recruited offline. Targeted interventions of HIV prevention programs or services are recommended when designing preventive interventions to be delivered via the Internet.