INTRODUCTION: Antiretroviral treatment for HIV generates dyslipidemia, which is associated with cardiovascular risk and atherosclerosis. OBJECTIVE: To compare antiretroviral agents effects on lipids in patients with HIV-AIDS. METHODS: Retrospective cohort. The lipid profiles of patients receiving efavirenz (EFV) vs. atazanavir (ATV) with a zidovudine + lamivudine backbone for 36 months were compared. RESULTS: 212 patients were included in the study. From baseline to month 36, HDL increase in the group of patients treated with ATV was higher in comparison with that of patients on EFV (8.33 vs. 4.26; p < 0.01); a difference in triglycerides was observed between groups, with a decrease of 19.06 mg/dL in patients on ATV and an increase of 40.62 mg/dL in those who received EFV (p < 0.001). Mean difference in total and LDL-cholesterol change between both treatments was not significant (p = 0.32 and p = 0.951, respectively). CONCLUSIONS: ATV-containing regimens were associated with more favorable changes in triglyceride and HDL levels than EFV regimens. This benefit could be associated with a reduction in long-term cardiovascular risk; this relationship requires further study.