Information on the dynamics, frequency, and structure of congenital malformations (CMs) and chromosomal diseases in two generations of rural populations from the Semipalatinsk region was obtained for the first time. The tests performed in the Semipalatinsk nuclear test site (STS) for many years were demonstrated to deteriorate the genetic health of the populations of the zones of extreme and maximum radiation risks. Mutagenic and teratogenic effects of long-term ionizing irradiation were detected. These were mainly expressed as an increase in the frequencies of strictly registered CMs (SR CMs), including the Down syndrome, multiple malformations (MMs) and microcephaly (1.45 +/- 0.11, 1.39 +/- 0.01, and 0.77 +/- 0.05 per 1000 births, respectively). SR CMs exhibited linear trends toward higher frequencies in two generations of exposed persons after surface nuclear tests in 1949-1963. Their frequency was strongly correlated with the effective population dose of radiation; the main population genetic parameters (inbreeding coefficient, endogamy index, etc.) had less pronounced effects on Cms.