This study aims to estimate the prevalence of congenital malformations and their correlation with socioeconomic and maternal variables. The design was cross-sectional, based on a sample of 9,386 postpartum women after admission for childbirth in maternity hospitals in the city of Rio de Janeiro, Brazil. Data were collected through interviews with mothers in the immediate postpartum, as well as by consulting the patient records of both the mothers and newborn infants. Prevalence of congenital malformations at birth was 1.7%, and minor malformations were the most frequent. Neural tube defects were the most frequent major malformations. According to multivariate analysis, congenital malformations were statistically associated with: maternity hospitals belonging to or outsourced by the Unified National Health System (SUS) and inadequate prenatal care (¾ 3 visits). This study highlights the importance of measures for health promotion and disease prevention in childbearing-age women, with special attention to prenatal care and childbirth, which can directly influence neonatal indicators and prevention of birth defects.