In connection with the drastically changed the human environment, including in connection with pollution by mutagenic and teratogenic factors of different origin, the majority of the population, including in Ukraine, is posed in different living conditions in comparison with previous generations. The recognizance of epigenetic impacts and the possibility of their inheritance significantly increased the role of environmental factors in ensuring human health of both present and future generations. There has been proposed the system of assessment of the status and reproduction of the genofond of the population consisting of assessment of the level of natality, determination of the proportion of persons of optimal reproductive age and children, calculation of the frequency and risk of congenital malformations, spontaneous abortions of the first trimester of gestation, infertile marriages, as well as identification of priority risk factors of formation of pathology, analysis of anthropometric parameters of newborns and comparison them with data characterizing the previous generation. The work of the system is based on existing statistical databases, it requires qualitative level diagnostics and the accounting of congenital malformations, as well as creation registries of congenital malformations, spontaneous abortions and infertile marriages.