We screened rat brain cDNA libraries and used 5' rapid amplification of cDNA ends to clone two electrogenic Na+-HCO3- cotransporter (NBC) isoforms from rat brain (rb1NBC and rb2NBC). At the amino acid level, one clone (rb1NBC) is 96% identical to human pancreas NBC. The other clone (rb2NBC) is identical to rb1NBC except for 61 unique COOH-terminal amino acids, the result of a 97-bp deletion near the 3' end of the open-reading frame. Using RT-PCR, we confirmed that mRNA from rat brain contains this 97-bp deletion. Furthermore, we generated rabbit polyclonal antibodies that distinguish between the unique COOH-termini of rb1NBC (αrb1NBC) and rb2NBC (αrb2NBC). αrb1NBC labels an ~130-kDa protein predominantly from kidney, and αrb2NBC labels an ~130-kDa protein predominantly from brain. αrb2NBC labels a protein that is more highly expressed in cortical neurons than astrocytes cultured from rat brain; αrb1NBC exhibits the opposite pattern. In expression studies, applying 1.5% CO2/10 mM HCO3- to Xenopus oocytes injected with rb2NBC cRNA causes 1) pH(i) to recover from the initial CO2- induced acidification and 2) the cell to hyperpolarize. Subsequently, removing external Na+ reverses the phi increase and elicits a rapid depolarization. In the presence of 450 μM DIDS, removing external Na+ has no effect on phi and elicits a small hyperpolarization. The rate of the phi decrease elicited by removing Na+ is insensitive to removing external Cl-. Thus rb2NBC is a DIDS-sensitive, electrogenic NBC that is predominantly expressed in brain of at least rat.