Phytoestrogens are non-steroid plant polyphenolic molecules that could bind to estrogen receptors and have been considered as endocrine disruptors, capable of acting either as agonist or antagonist of animal estrogens. Genistein is the most studied phytoestrogen contained in soy and soy-derived products. Negative effects on reproductive health from the gestational up to adulthood are profusely documented. It has a regulatory effect on the Hypophysis-Hypothalamus-Gonad Axis, the main endocrine regulatory system of animal reproduction. Several studies indicate that genistein-containing food or its experimental administration is capable of altering the endocrine system physiology through the HHG axis. The basic mechanisms of the several alterations in the HHG axis induced by genistein and their effects on the reproductive capability of the exposed animals are reviewed.