There is growing interest in the potential health threats posed by endocrine-disrupting chemicals (EDCs) to the reproductive system. Soybean is the most important dietary source of isoflavones, an important class of phytoestrogen. While consumption of soy food or phytoestrogen supplements has been frequently associated with beneficial health effects, the potentially adverse effects on development, fertility, and the reproductive and endocrine systems are likely underappreciated. Here we review the available epidemiological, clinical and animal data on the effects of soy and phytoestrogens on the development and function of the male and female reproductive system, and weigh the evidence as to their detrimental impact.