Inappropriate exposure of neonatal sheep to estrogen during critical developmental periods inhibits or retards endometrial gland morphogenesis and reduces uterine growth. Studies were conducted to identify mechanisms mediating estrogen disruption of neonatal ovine uterine development by analysis of candidate growth factor systems and using suppression subtraction hybridization (SSH). In study 1, sheep were exposed either to corn oil as a control or to estradiol valerate (EV) from birth to Postnatal Day (PND) 14, which ablated endometrial gland development. Estradiol valerate decreased uterine FGF7 (fibroblast growth factor 7) and MET (hepatocyte growth factor receptor) expression and increased INHBA (inhibin βA). The SSH identified a number of genes responsive to EV, which included GSTM3 (glutathione S-transferase), IDH1 (cytosolic NADP-isocitrate dehydrogenase), PECI (peroxisomal D₃,D₂-enoyl-coenzyme A isomerase), OAS1 (2′,5′-oligoadenylate 40/46-kDa synthetase), IGFBP3 (insulin-like growth factor-binding protein-3), TEGT (testis-enhanced gene transcript), CXCL10 (interferon-γ-inducible protein 10), and IGLV (immunoglobulin V). These mRNAs were expressed predominantly in the endometrial epithelia (GSTM3, IDH1, PEC1, OAS1, and TEGT), stroma (IGFBP3), or immune cells (CXCL10 and IGLV). In study 2, effects of estrogen exposure on uterine gene expression were determined during three different critical developmental periods (PNDs 0–14, 14– 28, and 42–56). Estrogen exposure decreased expression of the SSH-identified genes, particularly those from PNDs 0–14. These studies suggest that estrogen disruption of postnatal uterine development involves period-specific effects on expression of genes predominantly in the endometrial epithelium. The SSH-identified, estrogen-disrupted genes represent new candidate regulators of postnatal endometrial adenogenesis.