Endometriosis, one of the most frequent diseases in gynecology, is a benign but invasive and metastatic disease. The altered expression of E-cadherin may play an important role in developing endometriosis. In this paper, we discuss the association of three single nucleotide polymorphisms (SNPs) on the E-cadherin gene and risk of endometriosis. We examined the genotype frequency of three polymorphisms in 152 endometriosis patients and 189 control women. There was a significant difference in the frequency of the E-cadherin 3 '-UTR C -> T genotypes between endometriosis and controls (P= 0.01). The frequency of the C allele in patients (71.1 %) was significantly higher than in the controls (63.8%; P= 0.04). When compared with the T/T+ T/C genotypes, the C/C genotype had a significantly increased susceptibility to endometriosis, with an adjusted odds ratio of 1.79 (95% confidence interval= 1.17-2.76). No significant difference was found between endometriosis and control women on two polymorphisms (- 160 C - A, - 347 G -> GA) at the gene promoter region of E-cadherin. The - 160 C - A and - 347 G - GA polymorphisms displayed linkage disequilibrium (D '= 0.999). The - 160 A/ - 347 GA haplotype was only detected in endometriosis patients (2 %). These data show a relation between the E-cadherin 3 '-UTR C -> T polymorphism, the - 160 A/ - 347 GA haplotype of two promoter polymorphisms and risk of endometriosis, suggesting a potential role in endometriosis development, at least in North Chinese women.