Background Young men who have sex with men (MSM), are a key population at higher risk of HIV infection yet they are underrepresented in research. We conducted a bio-behavioral survey to estimate HIV prevalence and associated risk factors among tertiary student MSM (TSMSM) in Nairobi, Kenya. Methods Between February and March 2021, 248 TSMSM aged ≥ 18 years who reported sex with another man in the past year participated in a respondent-driven sampling (RDS) based cross-sectional survey. Participants completed an electronically self-administered behavioral survey and provided a blood sample for HIV antibody testing, alongside urine, anorectal and oropharyngeal swabs for pooled testing of sexually transmitted infections using a multiplex nucleic acid amplification test. RDS-Analyst v.0.72 and Stata v.15 software were used for data analysis. Differences in proportions were examined using chi-square (χ2) test, and unweighted multivariate logistic regression was used to assess factors associated with HIV infection. Results HIV prevalence among study participants was 8.3%, whereas the weighted prevalence was 3.6% (95% CI: 1.3–6.0%). Median ages of participants, and at self-reported first anal sex with a man were 21(interquartile range [IQR] 20-22) and 18 (IQR 17-19) years, respectively. A majority (89.3%) of TSMSM owned a smart phone, 46.5% had ever used a geosocial networking app for MSM such as Grindr ® to find a sex partner, and a third (33.6%) met their last sex partner online. Almost three-quarters (71.3%) had > 1 male sex partner in the year before the survey. A third (34.3%) did not use condoms with their last sex partner, 21.2% received money from their last sex partner and 40.9% had taken alcohol/another drug during their last sexual encounter. HIV infection was associated with studying in private institutions (adjusted odds ratio[AOR] = 6.0; 95% confidence intervals [CI] : 1.2–30.0, p = 0.027), preferring a sex partner of any age—younger, same or older (AOR = 5.2; 95 CI: 1.1–25.2, p = 0.041), last sex partner being > 25 years (AOR = 6.4; 95% CI: 1.2–34.6, p = 0.030), meeting the last sex partner online (AOR = 4.2; 95% CI; 1.1–17.0, p = 0.043) and testing positive for Neisseria gonorrhea (AOR = 7.8; 95% CI: 2.0–29.9, p = 0.003). Conclusions HIV prevalence among TSMSM in Nairobi is alarmingly high, demonstrating a need for tailored prevention and control interventions for this young key population.
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