Among women who become pregnant after initiating highly active antiretroviral therapy (HAART), few data describe the effect of pregnancy and postpartum on adherence. We conducted a retrospective clinical cohort study among therapy-naive women (ages 18–45) initiating HAART in Johannesburg, South Africa. Among 7,510 women in our analysis, 896 experienced a pregnancy after starting HAART. Compared to non-pregnant periods of follow-up, there was an increased risk of non-adherence during the postpartum period (weighted risk ratio (RR): 1.46, 95% confidence interval (CI): 1.17, 1.82), but not during pregnancy itself (weighted RR: 0.95, 95% CI: 0.78, 1.17)