The human AE1 anion exchanger gene SLC4A1 encodes the Cl-/HCO3-exchangers of the erythrocyte and the Type Acid-secreting intercalated cell basolateral membrane. Mutations in SLC4A1 have been correspondingly linked with autosomal dominant hereditary spherocytotic anemia and with both dominant and recessive forms of distal renal tubular acidosis. Murine knockouts in the slc4a1Ae1 gene have also been generated, and lack erythroid and renal expression. However, intragenic polymorphic markers for the slc4a1 gene have been unavailable. Here we report that a previously identified CA repeat element of intron 13 of the murine Ae1 gene exhibits strain-specific length polymorphism.