Abstract Within the context of high neonatal mortality in sub‐Saharan Africa, a retrospective study was conducted on the prevalence of congenital malformations and the association between maternal risk factors and birth defects in rural populations of south‐eastern Gabon. Two populations were studied: a group of 3500 births recorded in rural area (Koula‐Moutou) and a second group of 4212 births in a semi‐rural area (Franceville) in Gabon. Our data showed an increasing prevalence in congenital anomalies from rural to urban areas ( P < 0.001). Maternal risk factors such as age > 35 years, multiparity and employment status were significantly associated with the levels of stillbirth. Together with abortions and stillbirths, congenital malformations require strong monitoring in rural and urban areas of sub‐Saharan Africa.