BACKGROUND: There are conflicting reports of sex differences in HIV treatment outcomes in Africa. We investigated sex disparities in treatment outcomes for adults on first line antiretroviral treatment (ART) in Nigeria. METHODS: We compared clinical and immunologic responses to ART between HIV-infected men (n=205) and women (n=140) enrolled in an ART program between June 2004 and December 2007, with follow-up through June 2014. We employed Kaplan-Meier estimates to examine differences in time to immunologic failure and loss to follow-up (LTFU), and generalized estimating equations to assess changes in CD4+ count by sex. RESULTS: Men had lower baseline mean CD4+ count compared to women (327.6 cells/µL vs 413.4, respectively, p<0.01). Women had significantly higher rates of increase in CD4+ count than men, even after adjusting for confounders, p<0.0001. There was no significant difference in LTFU by sex: LTFU rate was 2.47/1000 person-months (95% CI 1.6-3.9) in the first five years for men vs 1.98/1000 person-months (95% CI (1.3-3.0) for women. There was no difference in time to LTFU by sex over the study period. CONCLUSIONS: Women achieved better long-term immune response to ART at baseline and during treatment, but had similar rates of long-term retention in care to men. Targeted efforts are needed to improve immune outcomes in men in our setting.