Root resorption lacunae are principally formed by odontoclasts. While these cells develop from the same origin as osteoclasts, odontoclasts normally have fewer nuclei and a less clear zone compared with osteoclasts. We therefore, hypothesized that odontoclasts possess less differentiation in matrix resorption characteristics than osteoclasts. To test our hypothesis, we compared the TRAP-positive area and the expression patterns of two important proteolytic enzymes, cathepsin K and matrix metalloproteinase-9 (MMP-9), between odontoclasts and osteoclasts. We focused on physiological root resorption in the rat molar, which is a useful experimental model for estimating odontoclasts and osteoclasts. Observations showed the number of nuclei and the TRAP-positive area of odontoclasts to be significantly less compared with osteoclasts. Using in situ hybridization and double labeling fluorescence in situ hybridization showed the majority of odontoclasts to express both cathepsin K and MMP-9, especially 4 and 5 weeks of age, when physiological root resorption occurs actively. Moreover, putative precursor cells of odontoclasts, which typically appeared in the middle of the periodontal ligament at 3 weeks of age, expressed both enzymes. In contrast, the majority of matured osteoclasts expressed only cathepsin K but not MMP-9. We suggest that odontoclasts are comparable to osteoclasts with less differentiation with regard to the expression of proteolytic enzymes.