The present studies demonstrate cloning, sequencing, tissue distribution, and functional expression of a Na+/H+ exchanger which was isolated from a rat intestinal cDNA library. The cloned cDNA recognizes two transcripts in poly(A)+ RNA from the stomach, jejunum, ileum, liver, large intestine, and uterus. Based on deduced amino acid sequences, this clone shares sequence homology with the other known Na+/H+ exchanger isoforms (NHE-1, NHE-3, and NHE-4) except for its 5' end. Overall, the protein exhibits 47.8%, 41.2%, and 56.2% amino acid sequence identity to NHE-1, NHE-3, and NHE-4, respectively. The hydropathy profile of the predicted protein shows 10 transmembrane domains, suggesting a protein with transport characteristics. The tissue distribution differs from that of the other Na+/H+ exchanger isoforms. The cDNA hybridizes to two closely related transcripts in the mRNA of these tissues, which suggests that the predominant transcript of this clone is alternatively spliced. Transfection of this cDNA into Na+/H+ exchanger-deficient mutant fibroblasts (PS120 cells) results in functional Na+/H+ exchange activity. These data suggest that we have cloned a member of the Na+/H+ exchanger family with tissue-specific expression. We suggest the designation of NHE-2 for this Na+/H+ exchanger.