To explore functions of anion exchanger 2 (Ae2) in the development of bones and teeth we examined the distribution of Ae2 in cells involved in formation of teeth and surrounding bone in young hamsters, mice and rats. In all three species strongest immunostaining for Ae2 was obtained in basolateral membranes of maturation ameloblasts and in osteoclasts resorbing bone. In hamsters a weaker staining was also seen in the Golgi apparatus of secretory ameloblasts, young osteoblasts and osteocytes, odontoblasts and fibroblasts of the forming periodontal ligament. In adult Ae2a,b-/- mice, in which Ae2 targeted disruption precluded the expression of Ae2a, Ae2b1 and Ae2b2 isoforms, the immunostaining for Ae2 in ameloblasts and osteoclasts was totally abolished. Enamel formation was abnormal but teeth erupted, osteoclasts in jaw bone were functional and structure of dentin and bone was normal. In another mouse model, Ae2-/- mice in which expression of all five Ae2 isoforms was disrupted, teeth failed to erupt and the alveolar bone proved poorly formed with giant but apparently functional osteoclasts. Our data indicate that basolaterally located Ae2a, Ae2b1, or Ae2b2 (or a combination of these) is present in maturation ameloblasts critical for the cells’ normal functioning. While isoforms of AE2 were also present in basolateral membranes of osteoclasts they proved not critical to osteoclast resorption of orofacial bone. Poorly formed bone and the failure of teeth to erupt seen in the Ae2-/- mice with gene disruption affecting all isoforms may result from secondary (systemic) changes that are different from Ae2a,b-/- mice.