Isoflavonoids are a class of secondary metabolites, which comprise amongst others the subclasses of isoflavones, isoflavans, pterocarpans and coumestans. Isoflavonoids are abundant in Leguminosae, and many of them can bind to the human estrogen receptor (hER) with affinities similar to or lower than that of estradiol. Dietary intake of these so-called phytoestrogens has been associated with positive effects on menopausal complaints, hormone-related cancers, and osteoporosis. Therefore, phytoestrogens are used as nutraceuticals in functional foods or food supplements. Most of the isoflavonoids show agonistic activity towards both hERα and hERβ, the extent of which is modulated by the substitution pattern of their skeleton (i.e. –OH, –OCH₃). Interestingly, substitutions consisting of a five-carbon prenyl group often seem to result in an antiestrogenic activity. There is growing evidence that the action of some of these prenylated isoflavonoids is tissue-specific, suggesting that they act like selective estrogen receptor modulators (SERMs), such as the well-known chemically synthesized raloxifene and tamoxifen. These so-called phytoSERMS might have high potential for realizing new food and pharma applications. In this review, the structural features of isoflavonoids (i.e. the kind of skeleton and prenylation (e.g. chain or pyran), position of the prenyl group on the skeleton, and the extent of prenylation (single, double)) are discussed in relation to their estrogenic activity. Anti-estrogenic and SERM activity of isoflavonoids was always associated with prenylation, but these activities did not seem to be confined to one particular kind/position of prenylation or isoflavonoid subclass. Few estrogens with agonistic activity were prenylated, but these were not tested for antagonistic activity; possibly, these molecules will turn out to be phytoSERMs as well. Furthermore, the data on the dietary occurrence, bioavailability and metabolism of prenylated isoflavonoids are discussed.