Congenital anal atresias were studied in a small geographical area in 225,752 consecutive births. For each of the 108 new cases studied during the period 1979 to 1995, more than 50 factors were compared in probands and in controls. The prevalence rate of congenital anal atresias was 4.8 per 10,000 births. Sex ratio was 0.96. Prenatal diagnosis was performed in 14 cases and 11 cases were induced abortions. The more common types of associated malformations in the 45 non syndromic affected cases with at least one major anomaly other than anal atresia were renal agenesia, genital anomalies and ventricular septal defect. At births infants with anal atresia and other malformations were smaller, weighted less and their head circumference was lower than in controls. Placental weight was also lower than in controls. Pregnancies with anal atresia were more often complicated by threatened abortion, oligoamnios and polyhydramnios. Mothers of children with congenital anal atresia took more often drugs during pregnancy than mothers of controls. Fathers of children with anal atresia were more often exposed to occupational hazards than fathers of controls. There was a significant association between anal atresia and consanguinity of parents (p < 0.05). The recurrence risk for first degree relatives of probands was 3.7%. First degree relatives of probands had more than twice the prevalence of non-anal atresia malformations than controls.