The presence of congenital malformations in infants born after IVF was studied from a register consisting of practically all infants born in Sweden after IVF, 1982--1997 (n = 9111). A further 64 infants were studied using only medical records. It is a nation-wide study and has a population-based control group (n = 1,690,577) and relevant potential confounders have been taken into account. There was an excess of congenital malformations registered in the Medical Birth Registry (n = 516, odds ratio = 1.47) but this excess disappeared when confounders were taken into consideration: year of birth, maternal age, parity, and period of unwanted childlessness (odds ratio = 0.89). For some specific conditions, an approximately 3-fold excess risk was seen: neural tube defects, alimentary atresia, omphalocele, and hypospadias (after intracytoplasmatic sperm injection). No excess risk for hypospadias was seen after standard IVF. Various explanations for these findings are discussed. It is postulated that the excess risk for alimentary atresia, like the excess risk for monozygotic twinning after IVF, is a direct consequence of the IVF procedure. The excess risk for hypospadias after ICSI may be related to paternal subfertility with a genetic background. The absolute risk for a congenital malformation in association with IVF is small.