Endometriosis affects >10% of women during their reproductive years, many of whom report high rates of spontaneous pregnancy loss (SPL). We examined whether gene polymorphisms in apolipoprotein E (APOE), which is involved in lipoprotein metabolism, are associated with endometriosis and/or endometriosis-associated infertility. We conducted a cross-sectional genetic association study of women surgically confirmed to have endometriosis (n = 345) and no surgical evidence of the disease (n = 266). Genotyping of APOE polymorphism (ε2, ε3, ε4) was conducted by polymerase chain reaction-restriction fragment length polymorphism followed by visualization of specific patterns by gel electrophoresis. Statistical significance of differences in genotype and allelic frequencies was assessed using Pearson's χ(2) test and Risk analysis. Overall, we found no association between APOE genotype and diagnosis of endometriosis. However, patients with endometriosis who reported at least one SPL were three times more likely to be ε2 carriers and 2-fold less likely to be ε4 carriers. Compared with ε3 carriers, patients with endometriosis who were ε2 carriers and had at least one live birth reported four times the rate of SPL, while ε4 carriers were <0.4-fold less likely to report an SPL. Our data suggest that there may be an association between APOE allelic frequency and SPL in patients with endometriosis, which appears to be independent of mechanisms associated with infertility, an intriguing observation that deserves further investigation.