Background: Alcohol use disorders (AUDs) may enhance the likelihood of risky sexual behaviors and the acquisition of sexually transmitted infections (STIs). Associations between AUDs with condomless anal intercourse (CAI) and STI/HIV prevalence were assessed among men who have sex with men (MSM) and transgender women (TW) in Lima, Peru. Methods: MSM and TW were eligible to participate based on a set of inclusion criteria which characterized them as high-risk. Participants completed a bio-behavioral survey. An AUDIT score ≥8 determined AUD presence. Recent STI diagnosis included rectal gonorrhea/chlamydia, syphilis, and/or new HIV infection within 6 months. Prevalence ratios (PR) were calculated using Poisson regression. Results: Among 312 MSM and 89 TW, 45% (181/401) had an AUD. Among those with an AUD, 164 (91%) were hazardous/harmful drinkers, and 17 (9%) had alcohol dependence. Higher CAI was reported by participants with an AUD vs. without, (82% vs. 72% albeit not significant). Reporting anal sex in two or more risky venues was associated with screening AUD positive vs. not (24% vs. 15%, p = 0.001). There was no difference in recent STI/HIV prevalence by AUD status (32% overall). In multivariable analysis, screening AUD positive was not associated with CAI or recent STI/HIV infection. Conclusions: In our sample AUDs were not associated with CAI or new HIV infection/recent STI. However higher prevalence of CAI, alcohol use at last sex, and anal sex in risky venues among those with AUDs suggests that interventions to reduce the harms of alcohol should be aimed toward specific contexts.