In conditions of continuous reduction of the population of Kherson region and the decline in fertility has witnessed the growth of population frequency of congenital malformations in a cohort of births (from 24.2 in 2000 to 35.1 in 2011 years). The rising prevalence of congenital malformations noted both in districts of the region (from 22.7% to 29,9) and in the regional centre (from 23.2 to 46,1). In the structure of the isolated malformations the largest share belongs congenital heart defects (28,5%), musculoskeletal (26,05%), urogenital systems (15,25%). Among the model malformations of the most common were hypospadias (frequency 1,9), the polydactyly (1,3), the down syndrome (1,1). In the Kherson region population frequency of cleft lip with or without palate, polydactyly, down syndrome was significantly higher compared with the corresponding data EUROCAT registries in Ukraine and countries of Europe.