Mammalian kidney is known to express a transport system specific for small peptides and pharmacologically active aminocephalosporins. This system is energized by a transmembrane electrochemical H+ gradient. Recently, a H(+)-coupled peptide transporter has been cloned from rabbit and human intestine (Fei et al. (1994) Nature 368, 563-566; Liang et al., J. Biol. Chem., in press). Functional studies have established that the renal peptide transport system is similar but not identical to its intestinal counterpart. Therefore, in an attempt to isolate the renal H+/peptide cotransporter cDNA, we screened a human kidney cDNA library with a probe derived from the rabbit intestinal H+/peptide cotransporter cDNA. This has resulted in the isolation of a positive clone with a 2190 bp long open reading frame. The predicted protein consists of 729 amino acids. Hydropathy analysis of the amino acid sequence indicates the presence of twelve putative transmembrane domains. The primary structure of this protein exhibits 50% identity and 70% similarity to the human intestinal H+/peptide cotransporter. Functional expression of the kidney cDNA in HeLa cells results in the induction of a H(+)-coupled transport system specific for small peptides and aminocephalosporins. Reverse transcription-coupled polymerase chain reaction demonstrates that the cloned transporter is expressed in human kidney but not in human intestine. This transporter, henceforth called PEPT 2, represents a new member in the growing family of H(+)-coupled transport systems in the mammalian plasma membrane.