Undetected sexually transmitted infections (STIs) pose health threats to people living with HIV and when combined with uncontrolled HIV can amplify HIV transmission. The current study screened 174 self-identified men under age 36 living with HIV and receiving antiretroviral therapy (ART) for urethral and rectal incident chlamydia and gonorrhea infections. Participants were also screened for biomarkers indicating alcohol and other drug use, subclinical genital inflammation, and HIV viral load. ART adherence and sexual behaviors were also assessed prospectively over 1 month. Results detected an undiagnosed STI in 32 (18%) individuals. Participants with a previously undetected STI had significantly greater HIV viremia than those who did not have an STI after controlling for several confounding variables. Participants with an undetected STI also engaged in greater condomless anal intercourse with HIV negative and unknown status partners, including partners to whom they had not disclosed their HIV status. These findings show that undetected STI are associated with incomplete ART adherence and unsuppressed HIV, all of which are important for preventing HIV transmission.