The multisubunit vacuolar-type proton-translocating ATPases (H⁺-ATPases) mediate the acidification of various intracellular organelles. In a subset of tissues, they also mediate H⁺ secretion at the plasma membrane. Two isoforms of the H⁺-ATPase B-subunit exist in humans; we have shown that mutations in ATP6V1B1, encoding the B1-isoform, cause the clinical condition distal renal tubular acidosis. Here we report the cloning and characterization of murine Atp6v1b1, which encodes a 513-amino acid (aa) protein with 93% identity to human ATP6V1B1. Genomic organization is conserved between the murine and human H⁺-ATPase B1-subunits, and Atp6v1b1 maps to a region of mouse chromosome 6 syntenic to human 2p13, the location of ATP6V1B1. Northern blotting detects a 2.2-kb Atp6v1b1 transcript in the kidney and testis, but not other major organs. In mouse kidney, the B1-subunit localizes to intercalated cells of the cortical and medullary collecting duct. B1 protein levels were not increased in either mouse renal cortex or medulla after either 2 or 7 days of oral acid loading. These results demonstrate that Atp6v1b1 encodes the murine ortholog of human ATP6V1B1 and provides a tool for future development of animal models based on manipulation of the Atp6v1b1 genomic locus.