Objective. To study the correlation of NAT2 gene mutations with endogenous intoxication and oxidative stress in patients with infertility and peritoneal endometriosis. Material and methods. 250 patients with peritoneal endometriosis and infertility were investigated. The level of endogenous intoxication and oxidative stress in association with NAT2 mutations was studied. Results. The results showed that gene NAT2 polymorphism is associated with changes in detoxication system and pro-antioxidant balance. In patients with NAT2 gene point mutations the increased level of middle-mass molecules, the decrease of endogenous intoxication index 280/254 and prooxidant balance disorders were detected. Non-pregnant patient with NAT2 gene mutations had the lowest rates of endogenous intoxication index 280/254. Index of oxidative stress was significantly lower. Conclusions. The patients with NAT2 point mutations have increased level of middle-mass molecules and decreased endogenous intoxication index. The natural detoxification system disorders may play an important role in the pathogenesis of endometriosis and infertility. The patients with gene NAT2 polimorphism have lower pregnancy rate after infertility treatment.