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The latest World Health Organization guidelines recommend replacing stavudine with tenofovir or zidovudine in first-line antiretroviral therapy in resource-limited settings. We report on outcomes and toxicities among patients on these different regimens in a routine treatment cohort in Lesotho.All adult patients initiating antiretroviral therapy from January 1, 2008, to December 31, 2008, were included in the analysis and followed until December 31, 2009. Choice of regimen was determined by clinical criteria.Of 1124 patient records analyzed, median age was 39 years, and the majority (67.7%) were women. Five hundred eighty-seven patients were started on tenofovir, 255 on zidovudine, and 282 on stavudine. Patients on zidovudine were more than twice as likely to experience a toxicity-driven regimen substitution compared with tenofovir (adjusted hazard ratio: 2.32, 95% confidence interval: 1.23 to 4.40); for patients on stavudine, the risk of a toxicity-driven regimen switch was almost 6 times higher than tenofovir (adjusted hazard ratio: 5.43, 95% confidence interval: 3.31 to 8.91).Our findings support the latest World Health Organization Guidelines, in particular the adoption of tenofovir in first line, given the advantages in terms of tolerability and availability as a once-daily formulation.