Study summary: The present study was designed to investigate the effect of perinatal exposure to the phytoestrogen genistein (found in soy) on the reproductive system of the male rat. Genistein has been reported to disrupt normal male sexual differentiation. Female rats were fed a phytoestrogen-free diet supplemented with either no genistein (free diet); a low dose of genistein (low diet); or a high dose of genistein (high diet) throughout their pregnancies and the entire lactation period. Anogenital distance (the distance between the anus and the base of the penis, a measure of male feminization) of male offspring was measured weekly from postnatal day two to day 21. At puberty (postnatal days 40 to 45), preputial separation (the separation of the prepuce from the glans penis, a measure of sexual maturation), and testis length and width were assessed. At age 70 days, reproductive organ masses, plasma testosterone concentration, sperm count and sexual behavior were also measured and evaluated. Exposure to genistein in the womb and while nursing was found to result in temporary, prepubertal urogenital abnormalities as of postnatal days 21 and 40. Males exposed to genistein had shorter anogenital distance and smaller testis size, as well as delayed preputial separation. Perinatal exposure to genistein also was found to cause long-term alterations in reproductive behavior; adult males were less likely to mount, intromit and ejaculate during mating tests. Males exposed to genistein also were found to have reduced testosterone concentrations in adulthood. The authors conclude that perinatal genistein exposure results in transient and lasting alterations in masculinization of the reproductive system.