Estrogen receptors (ERs) are transcription factors with two subtypes: estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ), which are essential for the maintenance of human health and play a regulatory role in common diseases such as breast cancer, osteoporosis, neurodegenerative disorders, liver injuries and lung cancers. A number of phytochemicals extracted from various fruits and vegetables have been demonstrated to exhibit estrogenic effects and are termed phytoestrogens. As modulators of ERs, phytoestrogens can be involved in the prevention and treatment of multiple diseases as complementary or alternative therapeutic agents and have a variety of health benefits for humans. This article reviews the health benefits of phytoestrogens in clinical and epidemiologic studies for several diseases and also provides a detailed description of the molecular mechanisms of their action. A brief comparison of the advantages and disadvantages of natural phytochemicals compared to synthetic drugs is also presented. The role of phytoestrogens in the treatment of diseases and human health requires further research to fully realize their therapeutic potential.