Objective: In April 2010, South Africa replaced stavudine with tenofovir in first-line antiretroviral therapy (ART) despite tenofovir’s higher cost. We examined treatment outcomes over 24 months amongst patients initiated on tenofovir-based vs. stavudine-based first-line regimens. Methods: Prospective cohort analysis of 3940 patients newly initiating either stavudine-based (April 2009 to March 2010) or tenofovir-based (April 2010 to March 2011) ART in Johannesburg, South Africa. Cox proportional hazards models and Fine and Gray’s competing risk regression accounting for death were used to model mortality and loss to follow-up, respectively. Linear and log-binomial regression were used to evaluate associations with immunologic response and unsuppressed virus (≥400 copies/ml), respectively. Results: About 1878 patients prescribed tenofovir and 2062 patients prescribed stavudine were included. One hundred and sixty-six (8.8%) tenofovir and 244 (11.8%) stavudine patients died. Three hundred and fifty (18.6%) tenofovir and 379 (18.4%) stavudine patients were lost to follow-up over 24 months on ART. Adjusted regression models showed tenofovir and stavudine were comparable regarding death, loss to follow-up, immunologic response and virologic status. Conclusions: We found no difference in mortality, loss to follow-up, immunological and virologic outcomes over the first 24-months on ART associated with tenofovir compared with stavudine.