Our study aimed to measure HIV prevalence and associated risk factors among men who have sex with men (MSM) in three regions of Paraguay in 2020. MSM were recruited for cross-sectional surveys in three regions of Paraguay using respondent-driven sampling. Interview were conducted face-to-face to collect demographic characteristics and risk and preventive behaviors. The analysis assessed HIV prevalence and associated risk factors in the three samples of MSM within each region. A total of 1,207 MSM were recruited, including 559 in Asunción-Central, 245 in Alto Paraná, and 403 in Caaguazú. HIV prevalence was 24.2% (95% CI 20.6-27.9) in Asunción-Central, 10.2% (95% CI 6.7-14.6) in Alto Paraná, and 3.2% (95% CI 1.7-5.4) in Caaguazú. In Asunción-Central, associations with HIV were age ≥25 years (1.86, 95% CI 1.15-3.00), being employed (1.82, 95% CI 1.07-3.11), self-reporting as homosexual (1.90, 95% CI 1.06-3.43), having sex with a known HIV-positive partner acquisition (4.19, 95% CI 2.37-7.43), self-perceived as being at higher risk for HIV acquisition (4.15, 95% CI 2.54-6.77), and able to access condoms and lubricants (1.82, 95% CI 1.08-3.05). In Alto Paraná, associations with HIV were self-reporting as homosexual (4.33, 95% CI 1.19-15.65) and having higher HIV knowledge (2.53, 95% CI 0.97-6.61). In Caaguazú, associations with HIV were self-reporting as homosexual (7.06, 95% CI 1.53-32.46) and being diagnosed with depression (4.68, 95% CI 0.89-24.43). HIV prevalence among MSM in Paraguay varied by region, being highest in the capital and major metropolitan area of Asunción-Central, followed by the border area of Alto Paraná. While being self-identified as homosexual was associated with HIV in all three regions, other associations differed, indicating prevention programs need to be tailored to the locale.
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