BACKGROUND: In the Andean Region, HIV and sexually transmitted infections (STI) are most prevalent among men who have sex with men (MSM), but incidence estimates and associated factors have never been prospectively assessed. METHODS: A cohort of 1056 high-risk HIV-negative MSM in Lima, Peru, were recruited during 1998-2000 (the ALASKA Cohort), and a nested case-control analysis was conducted between seroconverters and nonseroconverters, matched 1:3 by age and duration of follow-up for comparison of risk behaviors, acute retroviral symptoms, circumcision, and STI. RESULTS: During average follow-up of 335 days, 34 men seroconverted, providing a HIV incidence estimate of 3.5 per 100 person-years [95% confidence interval (CI): 2.3 to 4.7]. High syphilis (8.4 per 100 person-years, 95% CI: 6.7 to 10.1) and herpes simplex virus type 2 (HSV-2) infection (10.4 per 100 person-years, 95% CI: 8.6 to 11.9) incidence estimates were obtained. HIV seroconverters were more likely than men who remained seronegative to report fever ≥3 days (46% vs. 7%), to seek medical care (62% vs. 27%), and to have ≥1 casual partner (86.2% vs. 74.1%) since their last visit. HIV seroconverters also were more likely to have acquired syphilis or HSV-2 infection (31% vs. 8% among initially HSV-2-seronegative men) although they were less likely to be circumcised (4.2% vs. 20.6%, a nonsignificant difference). In multivariate analysis, incident syphilis or HSV-2 infection (odds ratio [OR]: 5.9, 95% CI: 1.5 to 22.7) and sex with any casual partner (OR: 4.8, 95% CI: 0.9 to 26.2) were associated with HIV seroconversion. CONCLUSIONS: STI that may cause anogenital ulcers are important risk factors for HIV acquisition among high-risk MSM in Lima, a population with a very high HIV incidence estimate. Synergistic interventions focusing in preventing both HIV and HSV-2, like male circumcision, are warranted to be assessed, especially in MSM populations with low levels of circumcision and high incidence estimates of ulcerative STI. © 2009 Lippincott Williams & Wilkins, Inc.