Many environmental chemicals are known endocrine disruptors (EDs). These have the potential to alter endocrine systems via various mechanisms that include binding to hormone receptors, thereby either mimicking or blocking the hormone actions and causing abnormal gene expression. Here, to elucidate the molecular mechanism(s) underlying the detrimental effects associated with the estrogenicity of these chemicals, we determined whether gene profiles were altered in rats exposed to 4-tert-octyphenol (OP) and diethylstilbestrol (DES) in utero. Pregnant rats were treated with a high dose of OP (600 mg/kg BW per day) or DES (500 microg/kg BW per day) at gestational days (GD) 17, 18 and 19. Both dams and neonates were euthanized at lactation day (LD) 5. The transcript profiles of uterine tissue were compared in treated versus control in both maternal and neonatal sites using cDNA microarray to determine the expression levels of approximately 13,000 genes and expressed sequence tags (ESTs). The expression levels of some known estrogen-responsive genes, i.e., complement component 3, epidermal growth factor receptor or c-fos oncogene and calbindin 3, as well as some other randomly selected genes, including general transcription factor IIa, transcription factor 4 and lymphocyte specific 1, were increased by OP and/or DES treatment in the uteri of both maternal and neonate groups. However, the magnitude of these alterations in gene expression differed markedly between dams and neonates, most likely reflecting the temporal susceptibility of the reproductive tract to estrogenic chemicals. Importantly, the altered gene patterns identified by microarray analysis were confirmed by RT-PCR and real-time RT-PCR. Fifteen primers were designed to amplify specific altered genes. These genes were selected for validation because of their markedly increased expression levels and they were classified on the basis of gene ontology. Overall, a high correlation was observed between microarray and real-time PCR data. Taken together, these results indicate that placental exposure to OP or DES may cause temporal changes in gene expression in the uteri of dams and neonates. Moreover, these findings may provide useful indicators of the adverse effects of EDs and prove particularly important in elucidating the effects of xenoestrogens on estrogen-responsive tissues, such as the developing reproductive tract.