Genetic factors are known to be associated with the development and progression of endometriosis, however the genes related with endometriosis have not been defined. Insulin-like growth factor binding proteins (IGFBPs) are believed to be involved in proliferation and apoptosis of cells which play an important role in pathophysiologic mechanism of endometriosis. This study aimed to determine the association between endometriosis and polymorphisms of IGFBP genes in Korean women. Case-control study The rs1995051, rs1065780 and Met253Ile single nucleotide polymorphism (SNP)s in the IGFBP1 gene and A(-672)G, A(-202)C and c.95C>G SNPs in the IGFBP3 gene were analyzed in 128 women with endometriosis and 108 normal control women by Taqman assay, PCR-RFLP and direct sequencing. Clinical stage was classified according to the revised American Fertility Society Classification The haplotype genotype composed by combination of three IGFBP1 gene polymorphisms was not related with endometriosis, while the haplotype genotype of IGFBP3 gene has a significant association with endometriosis. Women not carrying AAG (-672A/-202A/c.95G) haplotype allele of three IGFBP3 gene polymorphisms have 3.19-times higher risk of endometriosis compared with those with the AAG homozygotes, and this trend was found not in early endometriosis but in advanced endometriosis. The AAG haplotype allele of A(-672)G, A(-202)C and c.95C>G polymorphisms in IGFBP3 gene may be associated with advanced endometriosis in Korean women.