BACKGROUND: In sub-Saharan Africa, women are bearing a heavier burden than men in terms of rate of infection and socio-economic impact of HIV/AIDS. This study was aimed at assessing gender disparities in the socio-economic burden of HIV/AIDS. METHODS: This descriptive cross-sectional study was conducted among 422 HIV-positive adult patients attending an HIV clinic in Lagos, Nigeria, selected by multi-stage sampling and interviewed using a pretested, semi-structured questionnaire. Bivariate analysis was used to assess how the socioeconomic constructs differed by gender. RESULTS: This study revealed that females suffered more of the socio-economic consequences of having HIV/AIDS than males; cruelty and isolation were significantly higher among the females (p<0.0001), more females (50.0%) were discriminated against at the workplace compared to males (32.1%) (p=0.005), physical abuse (p=0.002) and extortion (p=0.029) were experienced by more of the females than the males. Also, the cost of care outside of antiretroviral therapy was significantly higher among the females (p= 0.002). CONCLUSION: Quantifying the social and economic disparities between HIV-infected men and women has shown that the burden is by far higher among women than men. Focused interventions are therefore needed to control the spread of the disease and improve the quality of life of HIV-infected women.