We investigated major congenital abnormalities in babies born in Al Jahra Hospital, Kuwait from January 2000 to December 2001. Of 7739 live and still births born over this period, 97 babies had major congenital malformations (12.5/1000 births): 49 (50.6%) babies had multiple system malformations, while 48 (49.4%) had single system anomalies. Of the 49 babies with multiple malformations, 21 (42.8%) had recognized syndromes, most of which were autosomal recessive and 17 had chromosomal aberrations. Isolated systems anomalies included central nervous system (12 cases), cardiovascular system (9 cases), skeletal system (7 cases) and gastrointestinal system (6 cases). Of the parents, 68% were consanguineous. Genetic factors were implicated in 79% of cases. Genetic services need to be provided as an effective means for the prevention of these disorders.