To know anogenital warts prevalence and its correlation with HIV infection in men who have sex with men (MSM) population in Surakarta, Indonesia. To identify risk factors associated with anogenital warts among MSM population in Surakarta, Indonesia. This cross-sectional study collects data from MSM population in Surakarta, Indonesia. Patients are MSM who joined monthly mobile clinic held by the health government of Surakarta and those who attend the Voluntary Consultation and Testing Clinic of Dr. Moewardi General Hospital. Risk factors were asked using questionnaire. Physical examination was used to diagnose anogenital warts, and took blood samples for HIV screening. From 190 subjects, 25 (13.1%) had anogenital warts, and 17 (8.9%) are HIV positive. Anogenital warts increase the odds of having HIV infection by 5.18 times. Risk factors that contribute to anogenital warts include age 25-34 years old (OR= 3,729) and a history of drug abuse (OR= 7.184). This research only uses simple physical examination to diagnose anogenital warts, and the small study subjects may not be representative of general MSM population in Indonesia. Age 25-34 years old and history of drug abuse are substantial risk factors for anogenital warts. Having anogenital warts infection increases the odds of acquiring HIV.  This study highlights the importance of STD screening especially in high-risk population such as MSM, which currently is still neglected by the Health Department of Indonesia.