Estrogen is an important steroid hormone with diverse functions in different parts of the human body. The developmental and physiological role of estrogen is mediated by estrogen receptor alpha (ER−alpha) and newly identified ER−beta. Regulation of expression of various important cellular oncogenes and tumor suppressor genes is a key component of estrogen and ER action. The expression of these genes is crucial in various processes such as cell cycle progression, mammary gland development, growth factor pathways and apoptosis. A very precise and accurate control of these genes is required for normal growth and functioning of cells. Aberrant expression of these genes through elevated expression, gene amplification or mutation may lead to induction and/or progression of different cancers including estrogen-dependent breast cancers. This review briefly describes the role of different genes that are regulated by estrogen in female reproductive tissues and breast cancer.