OBJECTIVE: To test the hypothesis that the endometrial response to Chorionic Gonadotrophin (CG) the major early, embryo derived signal, is altered by the presence of endometriosis. DESIGN: We assessed endometrial morphology, protein and gene expression changes occurring after in vivo intra-oviductal CG treatment of baboons with endometriosis. MATERIALS AND METHODS: Endometriosis was experimentally induced in female baboons (n=5) by intraperitoneal inoculation with menstrual endometrium. Three and six months following disease induction, human CG (hCG; 30IU/day) was infused into the oviduct via a subcutaneous osmotic mini-pump and polyurethane cannula. HCG infusion began on day 6 post ovulation (PO). Endometrial tissue was subsequently harvested by endometriectomy between days 9 to 11 PO, corresponding to the approximate time of implantation in the baboon. Control endometria were similarly harvested from disease free animals (n=6). Total RNA from each animal was hybridized to HumanRef-6 v3.0 Expression BeadChips (Illumina) containing 23,000 unique genes. Microarray data analyses were performed using BRB Array Tools. Verification of microarray data was performed using real time (RT) PCR; protein abundance changes were assayed by immunohistochemistry. All experimental procedures were approved by the Animal Care Committee of the University of Illinois, Chicago. RESULTS: Assessment of an early morphological response of baboon endometrium to hCG, the development of an epithelial plaque, revealed that the endometrium of all control animals was stimulated by hCG. However, an epithelial plaque was only elicited by hCG in two of five animals with endometriosis. Microarray analysis of endometria from baboons three and six months following induction of disease identified 22 and 116 genes, respectively, whose transcript levels differed more than 2-fold from those of control endometria (p<0.05). Several of these genes were previously shown to be regulated by hCG in disease free baboons. RT PCR analysis confirmed aberrant levels of LIF, complement factor C3, sFRP4 and SERPA3 in endometria of baboons with endometriosis. Immunohistochemical analysis revealed that this aberrant gene expression profile was not a result of altered CG receptor distribution in the endometrium of animals with endometriosis. CONCLUSIONS: An altered response to CG may prevent the acquisition of the full endometrial molecular repertoire necessary for implantation and may in part explain the implantation failure associated with endometriosis.