The two closely related, proton-coupled, electrogenic mammalian peptide transporters PEPT1 and PEPT2 differ substantially in substrate affinity and mode of function. The intestinal carrier PEPT1 has a lower affinity for most substrates than the isoform PEPT2 that is expressed in kidney, lung, brain and other tissues. A previous analysis of PEPT1-PEPT2 chimeras has suggested that the N-terminal half of the carrier proteins is important for substrate affinity. We constructed and analyzed new PEPT1-PEPT2 chimeras for identifying smaller segments within the N-terminal region of the transporter proteins that contribute to the kinetic properties. The first 59 or 91 amino-acid residues of PEPT1 were used to replace the corresponding region in PEPT2 leading to the chimeras CH3 and CH4, which could be analyzed when expressed in Xenopus laevis oocytes. Substrate affinities of both chimeras for the zwitterionic substrate D-Phe-Ala ranged between those that are characteristic for either PEPT1 or PEPT2, but when charged dipeptide substrates were employed, both chimeras possessed PEPT1-like affinities. The chimera CH3 carrying the N-terminal 59 amino-acid residues of PEPT1 exhibited a PEPT2-like phenotype with respect to pHout-dependency as well as to the current-voltage relationship of inward currents. In the chimera CH4 possessing the 91 amino-terminal residues of PEPT1, a pronounced alteration in the pHout-dependence was observed, with highest transport rates occurring at pH values as low as pH 4.0. Based on this analysis, we propose that the two identified aminoterminal regions in mammalian peptide carriers play an important role in determining the substrate affinity and also other characteristic features of the two transporter subtypes.