The aim of the study was to assess the incidence congenital malformation of congenital malformations in newborns in territories of the Bryansk region with different levels of radioactive, chemical and combined environmental pollution using official statistics for the period 2000-2017. Methods: Shapiro-Wilk test, White test, Wilcoxon T-test, Spearman rank correlation test and regression models were used to study associations between radioactive, chemical and combined pollution and the incidence of congenital malformations in the region and prognosis using the inverse relationship. Results. The incidence of polydactyly, multiple congenital malformations and the amount of de novo birth defects in newborns is significantly lower in the most ecologically favorable districts than in areas with radiation, chemical and combined pollution. For polydactyly - at the level of significance (p), 0.003-0.023 (decrease by 4.7-7.4 times), for the amount of multiple congenital malformations - 0.001-0.054 (2.5-6.8 times) and for amount of de novo birth defects - 0.0010.007 (3.5-4.6 times). Statistically significant differences were found in the incidence of multiple congenital malformations in the conditions of combined pollution in comparison with similar indicators in the territories of radioactive (2.2 times, p = 0.034) and chemical (1.9 times, p = 0.008) pollution (values 1.48; 0.67 and 0.78). A decrease in the long-term trend of frequency of multiple congenital malformations in the period 2000-2017 was revealed on the territories of combined pollution, and increase - on territories of radioactive and chemical pollution. Nevertheless, the predicted values of the frequency of multiple congenital malformations on the territories of combined pollution by 2018-2023 will significantly (p = 0.027) exceed the indicators of the territories of radioactive and chemical pollution by 39.6 and 45.7 % (values 1.18; 0.845; 0.81). Conclusions. Our results suggest synergistic effect of radiation and chemical pollution on the incidence of multiple congenital malformations.