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In resource-limited settings, there are only a few antiretroviral treatment (ART) options. Our objective was to evaluate the reasons for first-line ART changes in resource-limited settings.Prospective research cohort of patients initiating ART between April 2004 and April 2005 in Kampala, Uganda. The main endpoint was the substitution of at least 1 drug included in the initial combination.Five hundred Fifty-nine patients initiated on ART, 70% were female, median CD4+ count 98 (21-163) cells per microliter, median HIV RNA log10 5.4 (5.0-5.8). 413 (74%) patients were started on stavudine, lamivudine, and nevirapine, and 146 (36%) on zidovudine, lamivudine and efavirenz. One hundred Forty-eight (26.5%) had at least one treatment change (incidence rate 14.3 per 100 person-years; confidence interval: 12.2 to 16.9). The main reason for first treatment change was drug toxicity (n = 91, 61.5%). Stavudine accounted for the majority of the toxicities that led to drug substitution (n = 76, 84%). In the multivariate analysis, being female (P = 0.011) and being stage 3-4 as compared with 1-2 at ART initiation were predictive of stavudine substitution (P = 0.05). There was no difference in virologic outcome in patients who changed due to toxicity compared with those who did not.The majority of the treatment changes were due to stavudine-related toxicity. Long-term stavudine use is less well tolerated in women.