The multisubunit vacuolar-type H⁺ATPases mediate acidification of various intracellular organelles and in some tissues mediate H⁺ secretion across the plasma membrane. Mutations in the B1-subunit of the apical H⁺ATPase that secretes protons in the distal nephron cause distal renal tubular acidosis in humans, a condition characterized by metabolic acidosis with an inappropriately alkaline urine. To examine the detailed cellular and organismal physiology resulting from this mutation, we have generated mice deficient in the B1-subunit (Atp6v1b1^-/- mice). Urine pH is more alkaline and metabolic acidosis is more severe in Atp6v1b1^-/- mice after oral acid challenge, demonstrating a failure of normal urinary acidification. In Atp6v1b1^-/- mice, the normal urinary acidification induced by a lumen-negative potential in response to furosemide infusion is abolished. After an acute intracellular acidification, Na⁺-independent pH recovery rates of individual Atp6v1b1^-/- intercalated cells of the cortical collecting duct are markedly reduced and show no further decrease after treatment with the selective H⁺ATPase inhibitor concanamycin. Apical expression of the alternative B-subunit isoform, B2, is increased in Atp6v1b1^-/- medulla and colocalizes with the H⁺ATPase E-subunit; however, the greater severity of metabolic acidosis in Atp6v1b1^-/- mice after oral acid challenge indicates that the B2-subunit cannot fully functionally compensate for the loss of B1. Our results indicate that the B1 isoform is the major B-subunit isoform that incorporates into functional, plasma membrane H⁺ATPases in intercalated cells of the cortical collecting duct and is required for maximal urinary acidification.