BACKGROUND Borrelia infection is known to develop as a result of the bites of the ixodid ticks while the extremely difficult working conditions and low temperatures contribute to the development of chronic gonosteoarthritis (CGA) associated with ixodid tick-borne borreliosis (ITB) in the residents of the northern part of Siberia. OBJECTIVE The objective of the present study was to elucidate the frequency of occurrence of the synovial cells in the knee joints exhibiting the cytogenetic abnormalities with special reference to trisomy of chromosome 7 and the glutathione-S-transferase (GSTM1) gene polymorphism in the residents of the northern part of Siberia presenting with Lyme borreliosis (LB) whose genotype contains some alleles of the GSTM1 gene before and after the treatment of LB-associated CGA with the use of the radon bath therapy. The secondary objective was to compare the respective characteristics and the results of the treatment with those in the patients with post-traumatic gonosteoarthritis (PTGA) and to evaluate the influence of the above abnormalities on the severity of CGA. METHODS The study included 69 patients having gonosteoarthritis associated with ixodid tick-borne borreliosis and residing in the northern areas of Siberia; in addition, 52 other individuals presenting with post-traumatic CGA made up the control group. The synovial cells of the knee joints were obtained from all the participants of the study for their culturing, making preparations, and analyzing chromosomal aberrations. The polymorphism of the GSTM1 gene was investigated with the use of the real-time polymerase chain reaction. RESULTS The frequency of cytogenetic abnormalities in the synovial cells obtained from the group of patients presenting with LB-associated CGA who were the carriers of the homozygous mutant genotype GSTM1(0/0) was significantly higher than that in the patients having the normal genotype GSTM1(+) before the course of radon bath therapy. This treatment resulted in a significant decrease of the severity of pain syndrome and the improvement of the locomotor function of the affected joints in all groups of the patients involved in the study. The correlation analysis has demonstrated the significant positive correlation between the decrease in the frequency of occurrence of the synovial cells with trisomy of chromosome 7 and the severity of the pain syndrome. CONCLUSIONS The results of the present study give evidence of the significant association between the genetic polymorphism of the glutathione-S-transferase gene and the frequency of cytogenetic abnormalities in the synovial cells of the knee joints of the patients suffering from CGA associated with LB. The treatment based on radon bath therapy caused a considerable decrease in the frequency of synovial cells with trisomy of chromosome 7 which correlated with the reduction of the intensity of the pain syndrome in these patients.