Soy protein-based infant formulas (SF) are commonly used to feed infants during their first year of life. SF contains isoflavones, which influence cell proliferation, but their actions in the developing intestine have received little attention. Herein, the impact of soy isoflavones and SF on intestinal development and rotavirus (RV) infectivity is described. The isoflavone genistein has been found to reduce intestinal cell proliferation in vitro and in vivo in piglets without affecting intestinal enzyme activity or nutrient transport. However, isoflavones possess antiviral activity. The mix of isoflavones at the concentrations in SF, or genistin alone, inhibited RV infectivity by 40-60%. Thus, soy isoflavones are bioactive within the neonatal intestine and may reduce the severity of RV infections.