Non-specific effects of vaccination may be different for boys and girls. Due to the sequential administration of vaccines, it is difficult to separate the effect of different vaccines. We tested sex-specific effects of diphtheria, tetanus, pertussis (DTP) and polio vaccines and measles vaccines during the recent war (1998) in Guinea-Bissau when there was no functioning immunisation programme in the country. The study included 1491 children aged 1-17 months in four urban districts in Bissau. Vaccination status had been assessed in the study area in the 3 months before the war. The effect of DTP and polio vaccines was assessed for children who had not received measles vaccine. The effect of measles vaccine was evaluated for children aged 6-17 months. Compared with measles-unvaccinated children, measles-vaccinated children had lower mortality (mortality ratio (MR)=0.44 (95% CI 0.20-1.00)), the difference being marked for girls (0.25 (0.09-0.71)) but not for boys (0.84 (0.26-2.75)) (test of homogeneity, P=0.095). If measles cases were censored in the analysis, the mortality ratio for vaccinated and unvaccinated children was 0.38 (0.16-0.89). DTP and polio-vaccinated children did not have lower mortality than unvaccinated children. The female-male mortality ratio for DTP and polio-vaccinated children was 3.08 (1.11-8.56) and 0.63 (0.28-1.40) for measles-vaccinated children, a significant inversion of the ratios (test of homogeneity, P=0.013). The divergent female-male mortality ratios are unlikely to be explained by a selection bias going in different directions for different vaccines. The reduction associated with measles vaccination was unrelated to prevention against measles infection. Non-specific effects of vaccination should be assessed separately for boys and girls. Taking these effects into consideration may have implications for child mortality patterns in developing countries.