Background:Transgender women (TW) and men who have sex with men (MSM) are often conflated in HIV research and prevention programs, despite clear differences that exist in culture and behavior.Methods:We examined baseline data from a large treatment-as-prevention study among TW and MSM in Lima, Peru, to assess differences in risk behavior. Baseline assessment included HIV testing and a questionnaire including sociodemographics, sexual behavior, social venue attendance, and drug and alcohol use. Poisson regression with robust standard errors was used to calculate prevalence ratios adjusted for confounding variables [adjusted prevalence ratio (aPR)] and 95% confidence intervals (CIs) comparing the prevalence of covariates related to HIV risk in MSM and TW.Results:Overall, 310 TW and 2807 MSM participated between July 2013 and September 2015 and were included in this analysis. TW engaged in some protective sexual health practices more than MSM, including HIV testing in the last year (aPR = 1.62; 95% CI: 1.42 to 1.84) and condom use at the last sexual encounter (aPR = 1.20; 95% CI: 1.06 to 1.36). TW were more likely to have sex while using alcohol (aPR 1.15, 95% CI: 1.01 to 1.31) or drugs (aPR 2.24, 95% CI: 1.47 to 3.41), have alcohol dependency (aPR 1.38, 95% CI: 1.15 to 1.66), engage in receptive anal sex (aPR 1.31, 95% CI: 1.26 to 1.36), and have received money, gifts, or favors in exchange of anal sex (1.96, 95% CI: 1.74 to 2.20).Conclusions:TW and MSM exhibited distinct risk profiles, suggesting that interventions specifically targeted to each group may provide new opportunities for more effective HIV prevention programs.