Material-induced osteoinduction is reported in comparatively large animals such as dogs and pigs; however, it does not often occur in small animals such as rodents. In this study, we implanted porous calcium-deficient hydroxyapatite (CDHA) in the dorsal muscles of dogs and rats and compared the two species, with emphasis on multinucleated cells, by using hematoxylin and eosin (HE) staining, tartrate-resistant acid phosphatase (TRAP) staining, transmission electron microscope (TEM) observation, and reverse transcription-polymerase chain reaction (RT-PCR). In CDHA extracted from dogs, numerous TRAP-positive multinucleated cells were detected after 2 weeks and new bone formation was observed after 4 weeks. In contrast, in rats, only a small number of TRAP-positive cells were detected and no bone formation was observed within 6 weeks. CDHA was more degraded in dogs than in rats. TEM observation of the multinucleated cells in CDHA extracted from dogs after 3 weeks revealed osteoclast-like features such as ruffled borders. However, CDHA extracted from rats did not exhibit osteoclast-like features. RT-PCR evaluation showed that the expression of cathepsin K was higher in dogs than in rats. These results indicate that TRAP-positive cells might be one of the main factors responsible for the cross-species difference in material-induced osteoinduction.