First line treatment of hormone dependent breast cancer initially causes tumor regression but later results in adaptive changes and tumor re-growth. Responses to second line treatments occur but tumors again begin to progress after a period of 12???18??months. In depth understanding of the adaptive process would allow the identification of targets to abrogate the development of hormonal resistance and prolong the efficacy of endocrine therapy. We have developed a model system to examine adaptive changes in human MCF-7 breast cancer cells. Upon deprivation of estradiol for a prolonged period of time, a maneuver analogous to surgical oophorectomy in pre-menopausal women and use of aromatase inhibitors in post-menopausal patients, tumor cells adapt and become hypersensitive to estradiol. We reasoned that the expression pattern of multiple genes would change in response to estradiol deprivation and that cDNA microarrays would provide an efficient means of assessing these changes. Accordingly, we examined the transcriptional responses to estradiol in long-term estradiol deprived (LTED) MCF-7 cells with a cDNA microarray containing 1901 known genes and ESTs. To assess the changes induced by long-term estradiol deprivation, we compared the effects of estradiol administration in LTED cells with those in MCF-7 cells, which we had previously reported, and confirmed with real time PCR using the parental and LTED cells. Seven genes and one EST were induced by estradiol in LTED but not in wild type MCF-7 cells, whereas ten genes were down-regulated by estradiol only in LTED cells. The expression of seven genes increased concurrently and five decreased in response to estradiol in both cell types. From these observations, we generated testable hypotheses regarding several genes including DKFZP, RAP-1, ribosomal protein S6, and TM4SF1. Based upon the known functions of these genes and the patterns of observed changes, we postulate that divergent regulation of these genes may contribute to the different biologic responses to estrogen in these cell lines. These results provide targets for further mechanistic studies in our experimental system. Our findings indicate that long-term estradiol deprivation causes expression changes in multiple genes and emphasizes the complexity of the process of cellular adaptation.