We previously demonstrated that starvation markedly increased the amount of mRNA and protein levels of the intestinal H⁺/peptide cotransporter PEPT1 in rats, leading to altered pharmacokinetics of the PEPT1 substrates. In this study, the mechanism underlying this augmentation was investigated. We focused on the peroxisome proliferator-activated receptor α (PPAR), which plays a pivotal role in the adaptive response to fasting in the liver and other tissues. In 48-hour fasted rats, the expression level of PPAR mRNA in the small intestine markedly increased, accompanied with the elevation of serum free fatty acids, which are endogenous PPAR ligands. Oral administration of synthetic PPAR ligand WY-14643 to fed rats increased the mRNA level of intestinal PEPT1. Furthermore, treatment of the human intestinal model, Caco-2 cells, with WY-14643 resulted in enhanced PEPT1 mRNA expression and the uptake activity of glycylsarcosine. In the small intestine of PPAR null mice, augmentation of PEPT1 mRNA during fasting was completely abolished. In the kidney, fasting did not induce PEPT1 expression in both PPAR null and wild-type mice. Taken together, these results indicate that PPAR plays critical roles in fasting-induced intestinal PEPT1 expression. In addition to the well-established roles of PPAR, we propose a novel function of PPAR in the small intestine, that is, the regulation of nitrogen absorption through PEPT1 during fasting.