The objective of the study was to investigate the possible association between nausea and vomiting in early pregnancy and congenital abnormalities. The prevalence of medically-recorded severe nausea and vomiting in early pregnancy in cases with congenital abnormalities and their available matched population controls without any defect was compared in the population-based large data set of the Hungarian Case-Control Surveillance System of congenital abnormalities, 1980–1996. Of 22,843 cases with as 25 different congenital abnormality groups, 1,713 (7.5%) cases had mothers with medically recorded and treated severe nausea and vomiting during pregnancy. Of 38,151 matched population controls, 3,777 (9.9%) had mothers with severe nausea and vomiting (adjusted prevalence odds ratio (POR) with 95% CI: 0.74, 0.68–0.79). Five congenital abnormality groups: cleft lip with or without cleft palate (0.50, 0.37–0.70), posterior cleft palate (0.53, 0.32–0.89), renal a/dysgenesis (0.23, 0.06–0.96), obstructive defects of urinary tract (0.32, 0.18–0.58), and cardiovascular malformations (0.68, 0.57–0.81) had mothers with a lower prevalence of severe nausea and vomiting in pregnancy (adjusted PORs with 95% CI included in parentheses). Of 25 congenital abnormality groups, 22 had POR lower than 1. Thus in this study the mothers of cases with congenital abnormalities were 26% less likely to have had severe nausea and vomiting in early pregnancy than the mothers of population controls without congenital abnormalities. © 2006 Wiley-Liss, Inc.