To investigate the prevalence and genotype distribution of Chlamydia trachomatis infection among men who have sex with men (MSM), 145 MSM from two sauna settings in Shenzhen, China were invited to participate in this study during September 2008 and May 2009. Anorectal swab and urine samples were collected and tested for chlamydial infection, and positive samples were genotyped. The prevalence of anorectal chlamydial infection was 24% in the study population and was significantly associated with proctitis symptoms. Up to 50% of the anorectal infections were asymptomatic. The most prevalent genotypes were G (39%) and D (37%), followed by J (11%). Genotypes related to lymphogranuloma venereum were not found in the study population. The high prevalence of anorectal infection in MSM suggests the importance of detecting and treating the infection in this population.