This study assesses virologic response, safety, tolerability, and changes in health-related quality of life (HRQoL) in antiretroviral (ARV)-naive patients treated with 2 atazanavir (ATV)-based regimens over 96 weeks. Treatment-naive adult patients (n = 200) were randomized to receive either ATV 300 mg with ritonavir (RTV) 100 mg (ATV300/r, n = 95) or ATV 400 mg (ATV400; n = 105). At week 96, 75% of ATV300/r-treated and 70% of ATV400-treated patients achieved viral loads <400 copies/mL (difference estimate [95% confidence interval, CI] = 5.1 [-7.1 to 17.2]). Five and 20 patients, respectively, experienced virologic failure. Adverse event-related discontinuations occurred among 8% receiving ATV300/r and 3% receiving ATV400. Plasma lipid elevations were generally low. Both regimens were well tolerated and associated with sustained improvements in HRQoL. These findings demonstrate long-term efficacy, tolerability, and safety of both ATV300/r and ATV400 in ARV-naive patients through 96 weeks with improvements in HRQoL.