BACKGROUND: Adverse effects of combination antiretroviral therapy (CART) commonly result in treatment modification and poor adherence. METHODS: We investigated predictors of toxicity-related treatment modification during the first year of CART in 1318 antiretroviral-naive human immunodeficiency virus (HIV)-infected individuals from the Swiss HIV Cohort Study who began treatment between January 1, 2005, and June 30, 2008. RESULTS: The total rate of treatment modification was 41.5 (95% confidence interval [CI], 37.6-45.8) per 100 person-years. Of these, switches or discontinuations because of drug toxicity occurred at a rate of 22.4 (95% CI, 19.5-25.6) per 100 person-years. The most frequent toxic effects were gastrointestinal tract intolerance (28.9%), hypersensitivity (18.3%), central nervous system adverse events (17.3%), and hepatic events (11.5%). In the multivariate analysis, combined zidovudine and lamivudine (hazard ratio [HR], 2.71 [95% CI, 1.95-3.83]; P <.001), nevirapine (1.95 [1.01-3.81]; P =.050), comedication for an opportunistic infection (2.24 [1.19-4.21]; P =.01), advanced age (1.21 [1.03-1.40] per 10-year increase; P =.02), female sex (1.68 [1.14-2.48]; P =.009), nonwhite ethnicity (1.71 [1.18-2.47]; P =.005), higher baseline CD4 cell count (1.19 [1.10-1.28] per 100/microL increase; P <.001), and HIV-RNA of more than 5.0 log(10) copies/mL (1.47 [1.10-1.97]; P =.009) were associated with higher rates of treatment modification. Almost 90% of individuals with treatment-limiting toxic effects were switched to a new regimen, and 85% achieved virologic suppression to less than 50 copies/mL at 12 months compared with 87% of those continuing CART (P =.56). CONCLUSIONS: Drug toxicity remains a frequent reason for treatment modification; however, it does not affect treatment success. Close monitoring and management of adverse effects and drug-drug interactions are crucial for the durability of CART.