The aim of this study was to assess the genotoxic and cytotoxic effects that occur in miners working underground in rare metal ore mines at ionizing radiation levels within the maximum permissible concentration (MPC) standards using the buccal micronucleus cytome (BMCyt) assay. At the same time, we attempted to identify possible relationships between cytogenetic abnormalities in the buccal epithelium and such physiological indicators as cardiodynamics and the body mass index. The study involved a total of 269 individuals, 236 miners working underground in production related to the mining and enrichment of loparite ores and 33 non-exposed individuals (Russia, Murmansk region). Buccal micronucleus cytome assay and heart rate variability parameters were used. Micronucleus frequency was revealed to be a higher in the exposed group (8.3 ± 1.08‰) than in the non-exposed group (3.3 ± 0.49‰). The repair index showed a statistically significant increase in the non-exposed group (14.9 ± 2.90) compared with the exposed group (6.1 ± 0.74). The frequency of nuclear protrusions correlates significantly with the body mass index in the young miners (≤30 years (r = 0.45)). There is a negative relationship between the micronucleus frequency and the level of organism adaptation (r = −0.24), the vegetative regulation rate (r = −0.20) and the psycho-emotional state (r = −0.30) for miners older than 30 years. The results testify to the possible induction of clastogenic effects and a decrease in the level of reparation in the buccal epithelium cells due to the exposure of a various of production factors in the extraction of loparite ore.