Aim: With the increasing incidence of HIV and TB, motherless children are becoming a rapidly growing problem in Africa. However, few studies describe the survival patterns of these children. The aim of this study was to investigate the mortality of motherless children in urban and rural areas of Guinea‐Bissau. Methods: A historical cohort study was set up in urban and rural areas in Guinea‐Bissau. Motherless children were selected from two study cohorts under demographic surveillance since 1990. The relatives of 128 motherless children from the rural cohort and 192 from the urban area, as well as a total of 807 controls, were examined and interviewed. Results: Controlling for significant background factors revealed that motherless children had a markedly higher mortality than that of controls in both urban (mortality rate ratio (MR) 2.32 (95% confidence interval 1.11‐4.84)) and rural areas (MR = 4.16 (2.79‐6.22)). Virtually all the excess mortality occurred among children under 2 y of age when their mother died. Few motherless children had been provided with surrogate breastfeeding. Conclusions: Since nearly all children in Guinea are breastfed until 2 y of age, premature weaning may be one of the major causes of the higher mortality rates observed among motherless children.