Since estrogenic pollutants and phytoestrogens can cause the disorder of the reproductive system, the effects of a soybean milk product (Vegemil® containing 162 ppm isoflavones) on the feto-neonatal development, including male reproductive function, were investigated. Pregnant rats were fed the soybean milk (5% or 100% in drinking water) from gestational day (GD) 6 to parturition or to post-natal day (PND) 56. Specifically, the rats were divided into 4 groups: the control group (drinking water), the GD5% group (5% soybean milk during only the GD period), the GD-PND5% group (5% soybean milk during the GD and PND periods), and the GD-PND100% group (100% soybean milk instead of water during the GD and PND periods). During the gestational, lactational, and developmental periods, the reproductive and developmental parameters of dams and offspring were observed. Feeding soybean milk did not affect the birth and physical development of both male and female offspring. At PND57, the weights of the testes and epididymides of F1 males significantly increased by feeding a high concentration of the soybean milk (GD-PND100%). In addition, feeding of the soybean milk during both the GD and PND periods (GD-PND5% and GD-PND100%) enhanced the sperm counts and motility. The results indicate that soybean milk is safe for embryos, fetuses, and offspring, and improves the post-generational development of male reproductive function.