This study determined the types, patterns and prevalence of congenital malformation among the offspring of consanguineous and nonconsanguineous parents. In this prospective study of 3529 neonates delivered alive during a 1-year period, 109 had congenital malformations (3.09/1000 live births). The rate of congenital malformation was 2.0% among neonates from nonconsanguineous marriages and 7.0% from consanguineous marriages. The most common malformations were genitourinary (32.1%), musculoskeletal (22.0%) and cardiovascular (14.7%). Of the total malformed infants, 8.3% died within the neonatal period. Male infants were at greater risk for birth malformations. A history of congenital malformation was more common in siblings of consanguineous than nonconsanguineous marriages.