Phytoestrogens are a diverse group of plant-derived compounds that structurally or functionally mimic mammalian estrogens and show potential benefits for human health. An increase in phytoestrogen research over the past few decades has demonstrated the biological complexity of phytoestrogens, which belong to several different chemical classes and act through diverse mechanisms. Identification of the estrogen receptor beta (ER beta) and research into various ligand classes has enabled elucidation of molecular aspects important in selective ER binding. This article explores the structural characteristics and significance of functional groups as they relate to phytoestrogen selectivity for ER binding.