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Men who have sex with men (MSM) have become one of the most risky populations for HIV infection in China. Though several cross-sectional sero-prevalence studies have been conducted, the annual HIV incidence remains unknown in this population.We applied IgG-capture BED-enzyme immunoassay (BED-CEIA) to define the recent HIV-1 infections among MSM in Beijing in the years 2005 and 2006 and the annual HIV incidence was estimated. Results Overall, 1067 MSM samples were collected, including 526 samples in the year 2005 and 541 in 2006. In 2005, of 17 HIV seropositive samples, 7 were identified as recent HIV-1 infections and the estimated HIV infection incidence was 2.9% per year (95% CI, 0.8%-5.0%). In 2006, of 26 HIV seropositive samples, 9 were identified as recent HIV-1 infections and the estimated annual incidence was 3.6% (95% CI, 1.3%-5.9%), which was 0.7% higher than that in 2005. Individuals engaging in male group sexual intercourse (5.17% vs 0.87%, P=0.019) and having receptive anal sexual intercourse more than five times (2.79% vs 0.33%, P=0.047) in the past 6 months significantly increase the risk of being infected by HIV-1.A high level of annual HIV-1 infection incidence was observed among MSM in Beijing for the consecutive years 2005 and 2006 with a continuous increasing trend. The rising incidence and related high risk behavior among MSM alarmed the health authorities and calls for more effective intervention strategies among this population.