In studies evaluating the general US population, patients in primary care, and patients with chronic conditions, women consistently report poorer health-related quality of life (HRQoL) than men; however, studies evaluating HRQoL in patients with HIV/AIDS have not completely corroborated those findings. The objective of this study was to evaluate gender differences in HRQoL for participants in a large randomized trial comparing antiretroviral regimens. AIDS Clinical Trials Group (ACTG) 320 was a randomized, blinded, placebo-controlled trial comparing the 3-drug regimen of indinavir + zidovudine (or stavudine) + lamivudine with the 2-drug combination of zidovudine (or stavudine) + lamivudine in subjects with CD4 cell counts less than 200 cells/microl and no prior treatment with protease inhibitors. Nine quality of life domains scored on 0-100 scales were assessed using the ACTG QOL 601-602 Health Survey at 3 points in the trial: baseline, 24 weeks and 40 weeks. Differences between men and women in HRQoL scores were assessed using the Wilcoxon rank-sum test and generalized estimating equation (GEE) models. Overall, 202 females and 976 males were randomized to one of two treatment arms. Female participants were more likely to be black or Hispanic and tended to be younger. At baseline, females reported lower HRQoL scores than males in all of the domains except social functioning, and at week 40, women scored lower in all of the domains except overall health. In repeated measures models, women were found to score lower in all HRQoL domains except overall health, with significant differences of 3.5-6.7 points in 3 of the 9 quality of life domains: physical functioning, pain, and energy/fatigue. HRQoL scores improved for participants in the study over time and in response to potent treatment, and the improvements were similar for men and women. Women with HIV/AIDS report substantially poorer HRQoL than men with HIV/AIDS in several HRQoL domains. However, changes in domain scores over time and in response to treatment do not differ significantly by gender, implying that changes in domain scores may be better HRQoL outcomes to compare between HIV-infected men and women in clinical trials than mean domain scores.