PEPT2 is one of two identified proton-coupled oligopeptide transporters in mammals. It shows widespread expression within the organism. Highest expression is found in the kidney where it is supposed to mediate the reabsorption of filtered di- and tripeptides. To determine the physiological function of PEPT2 we have generated a Pept2-/-mouse line. For a comprehensive characterization of metabolic changes in response to loss of the peptide transporter PEPT2, kidney tissue samples of 5 PEPT2 null mice and wildtype control mice were submitted to transcriptome, proteome and metabolome profiling. cDNA microarray analysis identified 155 transcripts with significantly altered expression in transporter deficient animals. Proteome analysis by 2D-PAGE and MALDI-TOF-MS detected 29 proteins with altered steady state levels in knockout animals. Metabolite profiling revealed changes in levels of free amino acids, polyamines and intermediates of carbohydrate metabolism. These findings on changed metabolite levels were confirmed by differential expression of key enzymes of these metabolic pathways either at mRNA or protein level. Lower concentrations of cysteine, glycine and oxoproline in kidney tissue of the transporter-deficient animals together with increased expression of glutathione transferases at mRNA and protein level indicate that PEPT2 might be involved in renal glutathione metabolism.