Introduction: Congenital anomalies are a common cause of disability and mortality in newborns and their treatments involves high costs for the society. This study aimed to investigate the prevalence of congenital anomalies and their causes.

Materials and methods: This research was a descriptive-analytical study and the population included all the newborns in hospitals of the city of Ilam in 2011. Variables of abnormality type, birth status, and medical and genetic illness histories were included into the data collection forms. Data was analyzed through Chi-square tests and Fisher's exact test using SPSS software.

Results: Of 460 neonates, 5.4 percent (25 cases) had died at birth and 3.7 percent (16 infants) were born with a birth defect. 43.8 percent of malformed babies had a family history. 31.3 % of the malformed babies had genetic syndromes, whose parents had consanguineous marriage. 18.8% of babies with defects in the central nervous system and cardiovascular system showed a similar percentage of disorder. The defect in the urinary system, head and neck each accounted for 12.5 percent.

Conclusion: This study shows that consanguineous marriages can be the most common genetic cause of genetic syndromes.