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Faith Moyo,1 Charles Chasela,2,3 Alana T Brennan,1,4 Osman Ebrahim,5 Ian M Sanne,1,6 Lawrence Long,1 Denise Evans1 1Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 2Epidemiology and Biostatistics Department, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; 3Epidemiology and Strategic Information (ESI), HIV/AIDS/STIs and TB, Human Sciences Research Council, Pretoria, South Africa; 4Center for Global Health and Development, Boston University, Boston, MA, USA; 5Brenthurst Clinic, Parktown, South Africa; 6Right to Care, Helen Joseph Hospital, Westdene, Johannesburg, South Africa Background: Despite the widely documented success of antiretroviral therapy (ART), stakeholders continue to face the challenges of poor HIV treatment outcomes. While many studies have investigated patient-level causes of poor treatment outcomes, data on the effect of health systems on ART outcomes are scarce.Objective: We compare treatment outcomes among patients receiving HIV care and treatment at a public and private HIV clinic in Johannesburg, South Africa.Patients and methods: This was a retrospective cohort analysis of ART naïve adults (≥18.0 years), initiating ART at a public or private clinic in Johannesburg between July 01, 2007 and December 31, 2012. Cox proportional-hazards regression was used to identify baseline predictors of mortality and loss to follow-up (>3 months late for the last scheduled visit). Generalized estimating equations were used to determine predictors of failure to suppress viral load (≥400 copies/mL) while the Wilcoxon rank-sum test was used to compare the median absolute change in CD4 count from baseline to 12 months post-ART initiation.Results: 12,865 patients initiated ART at the public clinic compared to 610 at the private clinic. The patients were similar in terms of sex and age at initiation. Compared to public clinic patients, private clinic patients initiated ART at higher median CD4 counts (159 vs 113 cells/mm3) and World Health Organization stage I/II (76.1% vs 58.5%). Adjusted hazard models showed that compared to public clinic patients, private clinic patients were less likely to die (adjusted hazard ratio [aHR] 0.50; 95% confidence interval [CI] 0.35–0.70) but were at increased risk of loss to follow-up (aHR 1.80; 95% CI 1.59–2.03). By 12 months post-ART initiation, private clinic patients were less likely to have a detectable viral load (adjusted relative risk 0.65; 95% CI 0.49–0.88) and recorded higher median CD4 change from baseline (184 cells/mm3 interquartile range 101–300 vs 158 cells/mm3 interquartile range 91–244), when compared to public clinic patients.Conclusion: We identified differences in treatment outcomes between the two HIV clinics. Findings suggest that the type of clinic at which ART patients initiate and receive treatment can have an impact on treatment outcomes. Further research is necessary to provide more conclusive results. Keywords: health systems, attrition, HIV programs, viral suppression