Estrogen plays an important role in the growth and progression of human breast cancer. Understanding the whole picture of estrogen signaling is a very important goal towards clarifying the biology of this disease. On the other hand, hormonal therapy for breast cancer has been progressing rapidly with the advent of drugs such as selective estrogen receptor (ER) modulators and aromatase inhibitors. Prediction of individual response to these hormonal therapies is becoming important for the management of breast cancer patients. To help address these basic and clinical issues, we are developing several new tools such as the focused microarray and the green fluorescent protein-reporter cell system. We first carried out expression profiling of approximately 10,000 genes in ER-positive breast cancer cells. Based on the results, estrogen-responsive genes (ERG) were selected and a custom-made cDNA microarray consisting of 200 genes from a narrowed-down subset was produced. Using this microarray, we investigated various aspects of estrogen signaling such as the effect of estrogen-antagonists on ERG expression profile and functional analysis of ERbeta and novel estrogen responsive gene EGR3. Furthermore, expression levels of several candidate genes selected from the custom-array contents were analyzed by real-time RT-PCR and immunohistochemistry using breast cancer tissues to determine novel predictive factors for responsiveness to hormone therapy in primary breast cancer patients. Expression of several genes, such as HDAC6, significantly correlated with disease-free and overall survival of patients treated with adjuvant tamoxifen therapy. We are currently developing a new tool for analyzing the effects of novel aromatase inhibitors in individual breast cancer patients using estrogen-responsive element-green fluorescent protein-indicator cells. We hope that these approaches may provide not only new clues for elucidation of estrogen-dependent growth mechanisms of cancer, but also clinical benefits to patients by assessment of individual responses to endocrine therapy.