Clinical data on antiretroviral effectiveness in women are limited, especially long-term data, because women are usually underrepresented in clinical trials. This sub-analysis of a large European non-comparative, retrospective, observational cohort study evaluated gender differences in long-term outcomes in antiretroviral-experienced adult patients with HIV-1 infection switched to an ATV/r-based regimen between October 2004 and March 2007. Data were extracted from 3 European HIV databases every 6 months (maximum follow-up 5 years). Time to virological failure (VF), defined as two consecutive HIV-1 RNA≥50 c/mL or one HIV-1 RNA≥50 c/mL followed by treatment discontinuation (TD), and time to TD were analyzed using the Kaplan-Meier method. Associations of gender with VF and TD were analyzed using multivariate Cox proportional models. Safety and tolerability were evaluated. In total, 1294 patients (336 women, 958 men) were analyzed. No gender differences in time to VF were observed; at 3 years, the probability of not having VF was 0.59 (95%CI: 0.52, 0.65) and 0.63 (95%CI: 0.59, 0.67) for women and men, respectively. In multivariate analyses, women had a higher risk of TD than men (hazard ratio [HR], 1.54; 95%CI: 1.28, 1.85) but no increased risk of VF (HR, 1.06; 95%CI: 0.85, 1.33). Safety and tolerability were comparable between genders. In a clinical setting, long-term efficacy and safety outcomes of ATV/r-based regimens were similar by gender. Women had a higher risk of TD but no increased risk of VF. ATV/r is an effective and well-tolerated therapeutic option for treatment-experienced men and women with HIV-1 infection.