Anthropogenic impact on the biosphere has become one of the major factors dictating the conditions of our existence on the Earth. The study was aimed to perform comparative analysis of the rate of cytogenetic alterations, indicators of proliferation and destruction of the nucleus in the vaginal epithelium reflecting the reproductive health status of pregnant women aged 26–33 years living in conditions of radioactive, chemical and combined contamination of the territories of Bryansk Region. Cytogenetic status of 80 pregnant women divided into four groups, 20 individuals per group, was assessed using the micronucleus test. The rate of cytogenetic alterations, indicators of proliferation and destruction of the nucleus in the vaginal epithelium of pregnant women living in the environmentally disadvantaged territories was 1.9–4.9 times higher (p < 0.001) compared to that in women living in the environmentally safe (control) districts. The combined effects of radioactive and chemical contamination resulted in the significantly higher rate (increase from 12.8 to 81.4%) of cells with micronuclei, nuclear protrusions, binucleated cells, as well as cells with karyopyknosis and karyolysis compared to the effect of only one pollution factor. The findings are likely to show synergy of the effects of radiation and chemical factors on the cytogenetic status of pregnant women.