In various countries all over the world, the congenital malformations are among the leading causes of infant mortality and children disability. The historical approach is applied to consider epidemiological monitoring as a practice preceding the comprehensive analysis of causes and conditions of congenital malformations formation. The primary tasks of monitoring study are established and means of their implementation as well. The actual technique of registration and recording of various forms of the congenital malformations in children and its alternative are presented. The need of the coordinated activities of pediatric, medical genetic and epidemiological services in the organization and the execution of the monitoring in different regions of the country is emphasized.