Commercially available deproteinized cancellous bovine bone (DPBB) has been indicated as non-absorbable bone filling materials. Stoichiometric hydroxyapatite (HA) was not resorbed by osteoclasts while calcium-deficient and carbonate-rich apatite converted from octacalcium (OCP hydrolysate) was resorbed by osteoclasts. We analyzed the chemical composition of DPBB and compared the tissue reactions around two materials after implanting into mouse bone marrow. X-ray diffraction analysis and Fourier transform infrared spectroscopy showed that DPBB was a carbonate-rich apatite. Micro-CT analysis indicated the massive bone formation on both materials at 2 weeks, then gradually resorbed. At 12 weeks, osteoclasts were directly attached to both materials. The ultrastructure of ruffled borders on DPBB was identical to osteoclasts resorbing normal bone while ruffled border on OCP hydrolysate showed irregular shape. These results indicated that DPBB was the absorbed material and that the structure of ruffled border of osteoclasts might be regulated by the size or orientation of HA.