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Background and Objective: Congenital malformations are among important causes of morbidity and mortality in newborns. This study was done to determine the prevalence and pattern of congenital malformations in newborn. Materials and Methods: This descriptive study was done on 6089 newborns in maternity center in Rafsanjan, Iran during 2007-08. The newborns were examined by pediatricians and based on clinical examination the type of obvious of either minor or major malformations were recorded. Results: The 179 cases had at least a major or minor malformations. Over all the prevalence of malformations was 2.93%. The highest prevalence of obvious malformations was seen in the musculo-skeletal (43.5%), followed by genitourinary (22.9%) and cardiovascular systems (15.08%). There was significant relation between congenital malformations, gestational age and medicine used by mothers (P<0.05). Conclusion: The highest prevalence of obvious malformations was seen in the musculo-skeletal system.