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To compare the clinical, virological and immunological parameters of men and women at baseline and during antiretroviral treatment.Analysis over time of data collected prospectively from of 2620 patients in a large cohort of HIV-infected patients followed for 12 months after initiating a nelfinavir-based antiretroviral regimen.Women had higher CD4 cell counts (P < 0.001), lower viral load (P < 0.001) and more favourable clinical profile (P < 0.001) than men at baseline. Following treatment, antiretroviral drug-naive women had higher CD4 cell count (P = 0.01) over time than drug-naive men but similar virological responses (P = 0.6); among drug-experienced individuals, women had also better immunological (P = 0.06) and similar virological (P = 0.3) responses compared with men. Consequently, the viroimmunological profile was significantly more favourable in women at each time point. The rates of clinical progression or death were also lower in women (P = 0.008), although drug toxicity was observed more commonly in women (P = 0.09). The highest viroimmunological responses were observed during the first 3 months of therapy in both sexes, although virological responses were achieved up to the 6th month in drug-naive patients. Sex was significantly associated with clinical (P = 0.01), virological (P = 0.01) and immunological (P = 0.006) responses to antiretroviral treatment in multivariate analyses after adjustment for other variables. The differences between genders were not explained by different adherence to therapy.Women have more favourable clinical and viroimmunological patterns than men both at baseline and during antiretroviral treatment. Sex has a small but significant influence on the clinical and laboratory outcomes of HIV infection.