Due to the scarce data on the prevalence of sexually transmitted infections (STIs) among male-to-female trans-sex workers (TSW) and male sex workers (MSW) in Argentina, the present study aimed to estimate the incidence of human immunodeficiency virus (HIV), and the prevalence of HIV, hepatitis B virus (HBV), hepatitis C virus (HCV), and Treponema pallidum. Human papillomavirus (HPV) and Chlamydia trachomatis infections were tested among TSW. Two hundred and seventy-three TSW and 114 MSW were recruited by nongovernmental organizations. HIV incidence was estimated by STARHS (serologic testing algorithm for recent HIV seroconversion). HPV and C. trachomatis infections were tested in anal cells from TSW. TSW showed significantly higher prevalences of HIV (34.1 vs. 11.4%), HBV (40.2 vs. 22.0%), and T. pallidum (50.4 vs. 20.4%) than MSW. TSW tested positive for HPV in 111/114 cases and for C. trachomatis in 4/80 cases. Investigation of HBV, HCV, HIV, and T. pallidum co-infections showed that 72% of TSW and 39% of MSW had at least one STI. T. pallidum was the most frequent mono-infection. The estimated HIV incidence was 10.7 per 100 person-years (95% confidence interval (CI) 3.8-17.7) for TSW and 2.3 per 100 person-years (95% CI 0-6.7) for MSW. The high prevalence of STIs and the high incidence of HIV demonstrate the great vulnerability of these high-risk populations and indicate the urgent need for preventive strategies on intervention and facilitation of access to healthcare programs.