Endometriosis shows some characteristics of malignancy, including local invasion and aggressive spread to distant organs. The pathology of endometriosis may involve a complex interaction among genetic defects, DNA repairing defects and environmental factors. Since DNA repair capacity is closely related to the sustaining of the genomic stability, an XRCC1 Arg399Gln polymorphism was performed to evaluate the possible association with endometriosis in this paper. Recruited adult females were divided into two groups: [1] endometriosis group (n = 141) and [2] non-endometriosis group (n = 100). Genomic DNA was obtained from their peripheral leukocytes. DNA fragment coding XRCC1 Arg399Gln polymorphism was amplified by PCR and subsequently digested with MspI, and then the genotypes and allelic frequencies in both groups were compared. The genotype distribution and allelic frequency of XRCC1 Arg399Gln polymorphism was significantly different (P < 0.05). The partition of the “GG” homozygote in the patient group was greater than that in the control group, which means that for those people with more G allele, they will have higher risk for endometriosis. We concluded that XRCC1 Arg399Gln polymorphism is associated with higher susceptibility to endometriosis and XRCC1 Arg399Gln polymorphism might be a useful biomarker for endometriosis.