We have identified mRNA markers of estradiol and progesterone action in the mouse mammary gland and uterus to establish an in vivo model for the evaluation of novel and potentially tissue selective estrogens and progestins. Gene chip analysis of mRNA from ovariectomized (OVX) mice treated with vehicle (V), 17 beta-estradiol (E2), progesterone (P) or E2 + P for 7 days identified defensin beta 1 (Def beta 1) and indoleamine-pyrrole 2,3 dioxygenase (INDO) as markers of E2 and P action in the mammary gland, and serine protease inhibitor, Kazal type 3 (Spink3) and G protein-coupled receptor 105 (GPR105) as markers in the uterus. Def beta 1 and Spink3 are both upregulated by E2 + P, whereas INDO and GPR105 have a complementary profile of upregulation by E2 alone and suppression of the E2 effect by P. Quantitative RT-PCR analysis of mammary gland markers was concordant with histological changes. Using this model, medroxyprogesterone acetate (MPA) and tanaproget (TNPR), a novel nonsteroidal progesterone receptor agonist, were evaluated and found to have no marked tissue selectivity relative to progesterone. In addition, the ER alpha selective ligand propyl pyrazole triol (PPT) and the ER beta selective ligands ERB-041 and WAY-202196 were evaluated on the mammary gland endpoints of histology and Def beta 1 mRNA expression, and showed that ERa stimulation is necessary and sufficient for eliciting estradiol-mediated changes in the mammary gland. (c) 2006 Elsevier Ltd. All rights reserved.