Background: Periodontitis is an important oral disease. Stem cell therapy has found its way in treatment of many diseases. Objective: To evaluate the regenerative potential of periodontal ligament-derived stem cells (PDLSCs) and osteoblast differentiated from PDLSC in comparison with bone marrow-derived mesenchymal stem cells (BM-MSCs) and pre-osteoblasts in calvarial defects. Methods: After proving the existence of surface markers by flow cytometry, BM-MSCs were differentiated into osteoblasts. 5 defects were made on rabbit calvaria. 3 of them were first covered with collagen membrane and then with BM-MSCs, PDLSCs, and pre-osteoblasts. The 4^th defect was filled with collagen membrane and the 5^th one was served as control. After 4 weeks, histological (quantitative) and histomorphological (qualitative) surveys were performed. Results: Both cell lineages were positive for CD-90 cell marker, which was specifically related to stem cells. Alizarin red staining was done for showing mineral material. RT-PCR set up for the expression of Cbfa1 gene, BMP4 gene, and PGLAP gene, confirmed osteoblast differentiation. The findings indicated that although PDLSCs and pre-osteoblasts could be used for bone regeneration, the rate of regeneration in BM-MSCs-treated cavities was more significant (p<0.0001). Conclusion: The obtained results are probably attributable to the effective micro-environmental signals caused by different bone types and the rate of cell maturation. Key Words: Stem cell, Periodontium, Osteoblasts, Bone regeneration, Periodontitis, Periodontal ligament, Mouth diseases, Mesenchymal stem cells, Cell- and tissue-based therapy, Cell Lineage