Chlamydia trachomatis (CT) infection in the genitourinary tract is the most prevalent bacterial sexually transmitted disease (STD) worldwide. Genital chlamydial infection has a huge impact on sexual and reproductive health, and it is very common in developed and developing countries. The aim of this study is to determine the prevalence of Chlamydia trachomatis antigen and identify associated risk factors among HIV positive and HIV negative adult male patients attending National Institute of Medical Research (NIMR),Yaba, Lagos state,Nigeria. A total of 318 male subjects (159 HIV positive and 159 HIV negative) between the aged of 18-50 years and above were recruited for the study. A structured questionnaire was administered to the study participants to collection their sociodemographic and clinical information. Urine sample was collected from each participant and were analyzed for the presence of CT antigen using One-Step Chlamydia Rapid Diagnostic Test kit (GIMA, Italy) and the results were interpreted according to the manufacturer interpretation guide. Out of the 159 test samples of the HIV positive men analyzed for uro prevalence of CT antigen, 5 (1.6%) were positive for CT antigen, while 154 (48.4%) were negative. Meanwhile, out of the 159 control samples of the HIV negative men analyzed, only 1(0.3%) person was found to be positive for CT antigen. The remaining 158 subjects (49.7%) were negative. Risk factors that are very important for the occurrence of CT antigen amongst the study participants include: marital status (P=0.013) and number of sexual partner (P=0.014). The outcome of this study shows that CT antigen (1.6%) exists among HIV positive men attending the HIV clinic at National Institute of Medical Research (NIMR), Yaba, Lagos State. Hence, the clarion calls for the facility to include C. trachomatis antigen testing in their routine screening for HIV patients.