Endometriosis is clinically associated with pelvic pain and infertility, with implantation failure strongly suggested as an underlying cause for the observed infertility. Eutopic endometrium of women with endometriosis provides a unique experimental paradigm for investigation into molecular mechanisms of reproductive dysfunction and an opportunity to identify specific markers for this disease. We applied paralleled gene expression profiling using high-density oligonucleotide microarrays to investigate differentially regulated genes in endometrium from women with vs. without endometriosis. Fifteen endometrial biopsy samples (obtained during the window of implantation from eight subjects with and seven subjects without endometriosis) were processed for expression profiling on Affymetrix Hu95A microarrays. Data analysis was conducted with GeneChip Analysis Suite, version 4.01, and GeneSpring version 4.0.4. Nonparametric testing was applied, using a P value of 0.05, to assess statistical significance. Of the 12,686 genes analyzed, 91 genes were significantly increased more than 2-fold in their expression, and 115 genes were decreased more than 2-fold. Unsupervised clustering demonstrated down-regulation of several known cell adhesion molecules, endometrial epithelial secreted proteins, and proteins not previously known to be involved in the pathogenesis of endometriosis, as well as up-regulated genes. Selected dysregulated genes were randomly chosen and validated with RT-PCR and/or Northern/dot-blot analyses, and confirmed up-regulation of collagen ␣2 type I, 2.6-fold; bile salt export pump, 2.0-fold; and down-regulation of N-acetylglucosamine-6-O-sulfotransferase (important in synthesis of Lselectin ligands), 1.7-fold; glycodelin, 51.5-fold; integrin ␣2, E NDOMETRIOSIS IS AN estrogen-dependent, benign gynecologic disorder affecting 10 -15% of women of reproductive age (1, 2). It is characterized by endometrial tissue found outside of the uterus (primarily in the pelvic cavity) and is associated with pelvic pain and infertility. A recent meta-analysis of assisted reproductive outcomes revealed that women with endometriosis and infertility who undergo in vitro fertilization and embryo transfer (IVF-ET) have pregnancy rates that are about 50% of women who undergo IVF-ET for tubal factor infertility (3). Abnormalities in the endometrium resulting in failure of embryonic implantation are believed largely to account for the lower pregnancy rates in women with endometriosis. However, because the pathogenesis of endometriosis per se is uncertain, the basis of implantation failure in women with endometriosis has been difficult to define.The implantation process involves complex interactions between the embryo and the maternal endometrium, the latter of which is receptive to the embryo only during a restricted period, the window of implantation that spans cycle d 20 -24 (or LH ϩ 6 -10) (reviewed in Ref. 4). In humans, the implantation process begins with attachment of the emAbbreviations: BSEP, Bile salt export pump; C4BP, c...