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Adolescents experience disproportionately high rates of poor ART outcomes compared to adults despite prolonged use of antiretroviral therapy in Southern African treatment programs, presenting a significant challenge to national attempts to meet the UNAIDS 90-90-90 targets for 2020. This cohort study among adolescents aged 12–20 years accessing ART care at two urban public-sector clinics in Johannesburg between September and November 2013 aimed to identify factors potentially associated with poor attendance at clinic visits. Patients were followed up through routine medical records to identify missed visits (failing to attend clinic within 30 days of scheduled visit date) up to 2 years after enrolment. We enrolled 126 adolescents on ART for a median of 6.3 years (IQR: 2.7–8.4). A total of 47 (38%) adolescents missed a scheduled visit within 24 months of enrolment. Older adolescents (18–20 years) were more likely to miss a visit compared to adolescents aged 12–14 years (risk ratio (RR) = 1.72; 95% CI: 1.00–2.95). Those who were identified to have difficulty in taking medication (RR = 1.57; 95% CI: 1.13–2.18) as a barrier to care were more likely to miss a visit compared to adolescents who did not. Awareness of treatment fatigue, challenges to taking ART, and caregiver difficulties is important when considering interventions to improve treatment outcomes among adolescents. [ABSTRACT FROM AUTHOR]