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Introduction: The prison population in Peru exceeds 90,000 individuals, many of whom face conditions that increase their vulnerability to human immunodeficiency virus (HIV), such as exposure to illicit substances, risky sexual behaviors, and discrimination. Materials and Methods: A secondary analysis was carried out, using data from the 2016 national prison population census to identify factors associated with HIV risk in the incarcerated population of Peru. A total of 75,613 male inmates from prisons across the country participated, answering a comprehensive questionnaire consisting of 405 items. Multivariable regression Poisson models were used to calculate adjusted prevalence ratios (aPR) and 95% confidence intervals (CI). Results: Our findings revealed significant associations between HIV risk and sexual orientation, with homosexual (aPR: 5.50; CI: 2.62-11.56) and bisexual (aPR: 4.92; 95% CI: 2.26-10.72) individuals being at higher risk. Additionally, a history of tuberculosis (aPR: 2.82; 95% CI: 1.75-4.56) and sexually transmitted diseases (aPR 48.14; 95% CI: 31.07-74.56) were strongly correlated with increased HIV risk. Marital status, specifically being widowed, divorced, separated, or single, also showed a statistically significant association with HIV infection in both raw and adjusted regression models. Discussion: Our study highlights important risk factors for HIV infection among the male prison population in Peru. The identified associations will inform the development of effective health policies aimed at identifying and addressing HIV transmission within the country’s prisons. Furthermore, our findings provide a basis for future research in similar settings with a comparable male prison population profile.