This study investigated the effect of bone regeneration with dental pulp stem cells (DPSCs), deciduous tooth stem cells (DTSCs), or bone-marrow-derived mesenchymal stem cells (BMMSCs) for clinical study on hydroxyapatite-coated osseointegrated dental implants, using tissue engineering technology. In vitro, human DPSCs and DTSCs expressed STRO-1, CD13, CD29, CD 44, CD73, and osteogenic marker genes such as alkaline phosphatase, Runx2, and osteocalcin. In vivo, prepared bone defect model was implanted using graft materials as follows: platelet-rich plasma (PRP), PRP and canine BMMSCs (cBMMSCs), PRP and canine DPSCs (cDPSCs), PRP and puppy DTSCs (pDTSCs), and control (defect only). After 8 weeks, the dental implants were installed, and 16 weeks later the sections were evaluated histologically and histometrically. The cBMMSCs/PRP, cDPSCs/PRP, and pDTSCs/PRP groups had well-formed mature bone and neovascularization. Histometrically, the bone-implant contact was significantly different between the cBMMSCs/PRP, cDPSCs/PRP, pDTSCs/PRP groups, and the control and PRP groups (p < 0.01). These results demonstrated that these stem cells with PRP have the ability to form bone, and this bone formation activity might be useful for osseointegrated hydroxyapatite-coated dental implants with good levels of bone-implant contact.