Humans and wildlife are frequently exposed to mixtures of natural and synthetic endocrine-active compounds. To understand the impact of dietary phytoestrogen on the susceptibility to synthetic chemicals in the environment, we studied the effects of a binary mixture consisting of the isoflavone genistein and the pesticide methoxychlor on the development of the mammary gland. Sprague-Dawley rats were exposed to genistein at 800ppm, methoxychlor at 800ppm, or their combination through dietary administration to dams during pregnancy and lactation and to the offspring directly after weaning. At post-natal day (PND) 90, offspring rats were killed and their inguinal mammary glands collected for gene expression analysis utilizing the Clontech Atlas Rat 1.2 cDNA array, which contains probes for 1176 genes. Treatment with both genistein and methoxychlor altered gene expression profiles of the mammary glands in male rats, and the effects were more prominent in the combination treatment than the single-compound groups. Specific gene changes suggested that treatments affected the stromal and epithelial compartments of the mammary, involving genes controlling growth factor signaling, apoptosis, and tissue remodeling. This study demonstrates that dietary phytoestrogens in combination with a synthetic endocrine-active chemical can cause unique effects in endocrine-responsive tissues and highlights the importance of studying the effects of chemical combinations on the multiple biological processes underlying toxicological responses.