Background: Little is known about the risk for congenital malformations among infants born of women who are treated for functional gastrointestinal diseases during early pregnancy. Material and methods: Data from the Swedish national health registers were used to investigate possible associations between different drugs used at functional gastrointestinal diseases and occurrence of congenital malformations in the offspring. Drug use was ascertained by midwife interviews in early pregnancy recorded in the Medical Birth Register and the presence of congenital malformations by the use of three national health registers. Risk estimates were made with Mantel-Haenszel methodology and confidence interval estimates with Miettinen’s method. The effect of maternal characteristics and concomitant drug use was controlled. Women using drugs for inflammatory bowel disease were excluded from the analysis. Results: Among 1.5 million women 1282 (1301 infants) reported the use of drugs for functional gastrointestinal diseases in early pregnancy, 1048 (1062 infants) reported the use of antipropulsives, 3579 (3635 infants) the use of laxatives, and 13103 (13332 infants) the use of drugs for GERD. An increased risk for congenital malformations was found after the use of drugs for functional gastrointestinal diseases or of antipropulsives which could not be explained by concomitant drug use or maternal characteristics. It is unclear if it is a direct drug effect or is due to underlying disease. A specific effect was seen of dimethicone and of loperamide. No certain teratogenic effect was seen from laxatives or from most drugs used for GERD. An association between the use of sucralfate and congenital Conclusion: A small risk for congenital malformations is associated with maternal use of drugs for functional gastrointestinal diseases, if due to drug effects or to underlying pathology is unclear.