Objectives: The purpose of this study was to evaluate the influence of the follicle-stimulating hormone (FSH) receptor poymorphisms Asn680Ser and Thr307Ala on endometriosis in Turkish women. Methods: Polymorphic analysis of the FSH receptor gene was performed in 100 patients with endometriosis and 100 controls. Genomic DNA was obtained from peripheral blood leukocytes and polymorphisms were investigated using restriction fragment length polymorphism analysis. Results: There were no significant differences in genotype frequencies of FSH receptor gene between endometriosis patients and controls. When the patients were divided into two groups according to disease severity, we found that the patients with the SS (680 Ser/Ser) or AA (307 Ala/Ala) genotype were less likely to develop stage 3–4 endometriosis compared to the stage 1–2 endometriosis group (P = 0.004; OR: 0.177, 95 % CI 0.055–0.568 and P = 0.040; OR: 0.240, 95 % CI 0.061–0.938; respectively). Conclusions: The distributions of FSHR polymorphisms may not have an effect on endometriosis development but they are associated with the severity of the disease. The polymorphisms encoding SS at the position 680 and AA at the position 307 and the patients with the genotype that included alanine or serine were less likely to develop stage 3–4 endometriosis compared to the stage 1–2 endometriosis group.