The article covers the management of patients with internal genital endometriosis, in which the polymorphism of the glutathione-S-transferase genes has been diagnosed. The aim of our study was to select the optimal conservative method for treatment of internal genital endometriosis in women of reproductive age by developing complex therapy taking into account the polymorphism of the genes of the detoxification system. 102 patients with combined gynecological pathology were examined. All patients were subject to a dynamic clinical and laboratory examination. According to the presence of GSTT1 genes deletion, GSTM1 has established research groups and treatment. Analyzing the performed research, it was discovered that the clinical efficacy of complex treatment depended on the genotypes of patients. The presence of pathologically burdened alleles of genes GSTM1 and GSTT1 somewhat reduced the response to standard treatment in the second group of patients. However, when comparing the levels achieved in the group I of patients, it was determined that in general, the clinical effect of our proposed therapy was more pronounced than in the II and III clinical groups. Clinical research has proved the effectiveness of hormone therapy combined with immunomodulatory and target drug in the form of reducing recurrence and restoring fertility.