Endometriosis has been associated with aberrant methylation in the eutopic endometrium. Using a genome-wide methylation array, we identified differentially methylated genes in the endometrium from women with or without endometriosis. One hundred and twenty genes were significantly altered by >1.5-fold. In all, 59 genes were significantly hypermethylated and 61 genes were significantly hypomethylated. Changes in gene expression associated with the altered methylation status were validated using quantitative real-time polymerase chain reaction. A limited number of candidate genes are selectively methylated in the endometrium of women with endometriosis. Several genes not previously associated with endometriosis are aberrantly methylated and expressed. These include O-6-methylguanine-DNA methyltransferase, dual specificity phosphatase 22, cell division cycle associated 2, inhibitor of DNA binding 2, retinoblastoma binding protein 7, bone morphogenetic protein receptor, type 1B, tumor necrosis factor receptor 1B, zinc finger protein receptor 681, immunoglobulin superfamily, member 21, and tumor protein 73. Aberrant DNA methylation and gene expression of these genes may contribute to abnormal regulation of endometrial cell proliferation and function in women.