High levels of adherence have been identified as a key factor for effective pre-exposure prophylaxis medication (PrEP). Because PrEP is a new concept in HIV prevention, there are limited data on predictors of adherence, though initial findings indicate that sexual behavior could be an influencing factor. This study examines different aspects of sexual behavior and their associations with monthly rates and patterns of adherence. We enrolled 1147 HIV-negative individuals living in long-term serodiscordant relationships at three sites in Uganda. Sexual behavior was assessed via monthly in-person interviews and adherence was measured through electronic monitoring of pill bottle openings. We used generalized estimation equations to adjust for risk factors of low adherence to PrEP medication. Fifty-three percent of participants were male, 51% were aged between 18 and 34 years, the median number of years they had lived with the HIV-positive partner was 8.5 years and 24.2% were in polygamous relationships. Participants who had sex with other partners and also had less than 100% use of condoms were more than twice as likely to have less than 80% adherence (OR=2.48, 95%CI=1.70-3.62). Per electronic monitoring, 54.7% of cohort participants had at least one 72-hour consecutive gap in adherence. Participants who had sex with other partners and were also had also reported less than 100% use of condoms had a 50% increase in odds of having a 72-hour gap in adherence (OR=1.50, 95%CI=1.19-31.91). Low overall adherence and extended gaps in adherence were more common in participants that abstained from sex and those that reported sex outside their primary partnership. Despite high monthly adherence rates, many study participants had long periods of non-adherence during which they engaged in risky sexual behavior with potential for HIV acquisition.