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PhD (Molecular Medicine and Haematology), Faculty of Health Sciences, University of the Witwatersrand / Background: The availability of highly active antiretroviral (ARV) treatment in the South African government sector has reduced the morbidity and mortality associated with HIV-1 infection. However, ARV drug resistance and toxicity are major obstacles to achieving and maintaining virus suppression, but there is no provision for ARV drug resistance testing in the public sector. To date, most studies of ARV drug resistance in HIV-1 reverse transcriptase (RT) and protease (PR), are based on sequence data from HIV-1 subtype B, whereas subtype C is the predominant circulating subtype in South Africa. Moreover, host genetic polymorphisms associated with ARV drug toxicity have not been investigated in South African populations. This study evaluated viral and host genetic factors associated with ARV treatment outcome in 812 ARV drug-naive South African AIDS participants enrolled on the CIPRA-SA study from Johannesburg and Cape Town. Methodology: An affordable in-house genotyping protocol (subtype C specific) was established and validated to monitor the emergence of ARV drug resistance. This assay was used to genotype all CIPRA-SA participants failing the first- and second-line ARV drug regimens. Allellic discrimination assays to identify the G1344A, A6986G, G516T and C3435T SNPs in CYP3A4, 3A5, 2B6 and MDR-1, respectively, associated with ARV metabolism and absorption were performed. Results: The in-house ARV drug resistance assay successfully genotyped 95% of patient samples, including non-C subtypes from 8 African sites. Treatment failure was experienced in 371 participants, mainly due to toxicity (n=134) or virological failure (n=83). Overall, CIPRA-SA participants with a lower CD4+ T-cell count at study onset were more likely to experience viral failure. Genotyping using the in-house assay revealed that 6 participants had ARV drug resistance mutations at study entry. Treatment failure of 58 participants was a result of ARV drug resistance mutations, whereas 19 had no known ARV drug resistance mutations. The most frequent mutations were M184V (67%) and K103N (50%). K65R was present (3%) and one participant harboured TAMs. Longitudinal genotypic analysis showed that NNRTI mutations accumulated at a rate of one per three months left on failing therapy. No PR mutations were detected amongst participants experiencing second-line failure. The four SNPs analysed occured in similar frequencies between a background and the CIPRA-SA cohort. Furthermore, no statistically significant association could be found between these four SNPs and viral failure and/or toxicity. Conclusion: Overall, HIV-1 subtype C-infected individuals receiving ARV therapy develop many of the known subtype B drug resistance mutations. However, the ARV drug resistance patterns in the closely monitored CIPRA-SA cohort were less complex compared to published data from the region, confirming that more frequent viral load monitoring, genotyping, and a virological failure cut-off value of 1000 RNA copies/ml ensure a better prognosis, and preserve future ARV treatment options.