Lactic acid bacteria, either alive or dead, can improve villous atrophy caused by weaning in both piglets and mice. In this experiment, we tried to detect the molecules involved in this phenomenon with a real-time RT-PCR array approach. Weaning pups of mice were administered either a suspension of an Enterococcus faecalis EC-12 dried cell preparation (EC-12) or saline for 11 consecutive days after weaning. The jejunal and ileal villous heights were measured histologically, and the expression levels of 86 genes were analyzed for the jejunal and ileal epithelial cells and the lamina propria (LP). EC-12 induced significantly higher villous height in the jejunum and the ileum. Interleukin (IL)-6, fibroblast growth factor (FGF)-7, -10, and -22, and the platelet-derived growth factor (PDGF) beta in the jejunal and the ileal LP were the most enhanced genes by EC-12. The possible role of these molecules in the improvement of villous atrophy is discussed.