Background: The percentage of children born after IVF will continue to increase due to demographic changes such as increasing maternal age and new developments in assisted reproduction techniques. IVF conceptions may carry an increased risk of congenital malformations. Methods: We compared overall and specific congenital malformation rates calculated for IVF children (n = 4224) and naturally conceived children (n = 314 605), using records from the same Dutch national database for the years 1995 and 1996 and controlling for confounding maternal factors. Results: The overall crude odds ratio (OR) for the risk of any malformation for IVF children compared with naturally conceived children was 1.20 [95% confidence interval (CI): 1.01-1.43]. After correction for differences in maternal age, parity and ethnicity between the IVF and control population the OR was 1.03 (95% CI: 0.86-1.23). The crude OR for IVF children appeared higher for the cardiovascular organ system and for several specific minor congenital malformations. However, these could be chance findings due to comparison of many malformation categories or may result from remaining differences in ascertaining malformations between IVF and naturally conceived children. Conclusions: The small increase in overall congenital malformations observed in the IVF children appears to be attributable to differences in maternal characteristics and not to any aspect of the IVF procedure.