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It is reported that the rate of congenital malformations is about 2-3% at birth. They are one of the major causes of morbidity, mortality and disability in childhood are later in adulthood. The aim of this study was to determine the rate of gross congenital malformations that were preset at birth. The other factors studied were anatomic locations of anomalies, neonatal sex, race, maternal age and race. This study was a cross-sectional descriptive study, and the sample population was 10000 births. The rate of congenital malformations was 10.1/1000 in our sample 11.8/1000 in male and 7.5/1000 in female neonates. The rate of malformations in musculoskeletal system were 3.8 In CNS 2.8 and in urogenital system 2.5 per 1000 births. It was concluded that the most frequent malformations in CNS, musculoskeletal and urogenital system were cystic spina bifida, clubfoot and hypospadias respectively. The rate of malformations newborns were 14.5 per 1000, 8.5 per 1000 and 17 per 1000 birth in Turkman, native Fars and Sistan racial groups respectively. The results from this investigation showed that there were relations between rate of over malformations, races and sexes of individuals.