BACKGROUND: The sequence of routine immunisations may be important for childhood mortality. Three doses of diphtheria-tetanus-pertussis vaccine (DTP) should be given at 6, 10, and 14 weeks and measles vaccine (MV) at 9 months of age. The sequence is not always respected. We examined in-hospital mortality of children having received DTP with or after measles vaccine. SETTING: The only paediatric ward in Bissau, Guinea-Bissau. PARTICIPANTS: Children hospitalised during two periods in 1990-1996 and 2001-2002 who had received MV prior to hospitalisation. MAIN OUTCOME MEASURE: The all-cause case fatality at the hospital for children aged 6-17 months. RESULT: The case fatality was increased for children who had received DTP with or after measles vaccine compared with children who had received measles vaccine as the most recent vaccine, the ratio being 2.53 (1.37-4.67) and 1.77 (0.92-3.41) in the two periods, respectively. The combined estimate was 2.10 (1.34-3.28). These results were not explained by differences in nutritional status, number of doses of DTP or discharge policy. CONCLUSION: Administration of DTP with, or after MV, may reduce the beneficial effect of MV.