Objective In Guinea-Bissau, West Africa, we observed that having a smallpox vaccination scar was associated with lower HIV-1 prevalence, more strongly for women than men. If this represents a causal effect, the female/male HIV-1 prevalence ratio would increase for birth cohorts no longer receiving smallpox vaccination due to the phase-out of this vaccine. Design An ecological design using HIV surveys and information about smallpox vaccination coverage. Setting Urban and rural Guinea-Bissau. Participants Participants in HIV surveys were grouped into an age group with decreasing smallpox vaccination coverage (15-34 years) and an age group with steady smallpox vaccination coverage (≥35 years). Interventions The exposure of interest was the phase-out of the smallpox vaccine in Guinea-Bissau. Primary and secondary outcome measures HIV-1 prevalence. Results At both sites, the female/male HIV-1 prevalence ratio increased by calendar time for the age group with decreasing smallpox vaccination coverage; the combined female/male HIV-1 prevalence ratio among people aged 15-34 years was 1.00 (95% CI 0.17 to 5.99) in 1987-1990, 1.16 (95% CI 0.69 to 1.93) in 1996-1997, 2.32 (95% CI 1.51 to 3.56) in 2006-2007 (p value for no trend=0.04). There was no increase in the female-to-male HIV-1 prevalence ratio for the age group >35 years with steady smallpox vaccination coverage; 1.93 (95% CI 0.40 to 9.25) in 1987-1990, 1.32 (95% CI 0.83 to 2.10) in 1996-1997, 0.81 (95% CI 0.56 to 1.16) in 2006-2007 (p value for no trend=0.07). Conclusions Thus, data was compatible with the deduction that the phase-out of smallpox vaccination may have increased the susceptibility to HIV-1 relatively more for women than men. Hence, phasing out smallpox vaccination may have contributed to the global increase in the female/male HIV-1 prevalence ratio among young individuals. Due to the potential fallacies of ecological studies, the results should be interpreted carefully, and this hypothesis needs further assessment. If the hypothesis is true, studies of smallpox vaccination could inform HIV-1 vaccine research.