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Background: Chlamydia trachomatis (CT) infection is one of the most pervasive sexually transmitted infections and has high prevalence in urogenital and extra-urogenital sites among men who have sex with men (MSM). This study investigated anatomical site-specific prevalence and genotypes of CT among MSM recruited from three geographic areas in China.Methods: We collected urine specimens and anorectal, pharyngeal swab specimens from 379 MSM. CT infection was identified using polymerase chain reaction and CT genotyping was determined by sequences of the ompA gene.Results: The results indicated that the overall prevalence of CT infection was 18.2% (95% confidence intervals [CIs], 13.9-22.5%) and significantly different between the cities (p = 0.048). The infection was most common at the anorectal site (15.6, 95%CIs 11.6-19.5%) followed by urethral (3.2, 95%CIs 1.4-5.0%) and oropharyngeal sites (1.6, 95%CIs 0.3-2.9%). Genotypes D and G were the most common CT strains in this population but genotype D was significantly predominated in Nanjing while genotype G was in Wuhan. No genotype related to lymphogranuloma venereum was found. CT infection was significantly related to the infection of Neisseria gonorrhoeae (adjusted odds ratio [aOR] 14.27, 95%CIs 6.02-33.83, p < 0.001) and age. Men older than 40 years old were less likely to have a CT infection as compared to men under 30 years old (aOR 0.37, 95% CIs 0.15-0.93, p = 0.03).Conclusion: The high CT infection prevalence, particularly in the anorectal site, among MSM suggests the necessity to development an integrated CT screening and treatment program specifically focusing on this high-risk population. Surveillance of CT infections should be improved by including both infection and genotype based surveys into the current surveillance programs in China. [ABSTRACT FROM AUTHOR]