BACKGROUND Human dental stem cells have high proliferative potential for self-renewal that is important to the regenerative capacity of the tissue. Objective : The aim was to isolate human dental pulp stem cells (DPSC), periodontal ligament stem cells (PDLSC) and periapical follicle stem cells (PAFSC) for their potential role in tissue regeneration. METHODS In this experimental study, the postnatal stem cells were isolated from dental pulp, preapical follicle and periodontal ligament .The cells were stained for different stem cell markers by immunocytochemistry. To investigate the mesenchymal nature of cells, differentiation potential along osteoblastic and adipogenic lineages and gene expression profile were performed. For proliferation potential assay, Brdu staining and growth curve tests were performed. Finally, all three cell types were compared together regarding their proliferation, differentiation and displaying phenotype. RESULTS The isolated cell populations have similar fibroblastic like morphology and expressed all examined cell surface molecule markers. These cells were capable of differentiating into osteocyte with different capability and adipocyte with the same rate. PAFSCs showed more significant proliferation rate than others. Reverse transcriptase PCR (RT-PCR) for nanog, oct4, Alkaline phosphatase (ALP) and glyceraldehydes-3-phosphate dehydrogenease (GADPH) as control gene showed strong positive expression of these genes in all three isolated cell types. CONCLUSIONS PDLSCs, DPSCs and PAFSCs exist in various tissues of the teeth and can use as a source of mesenchymal stem cells for developing bioengineered organs and also in craniomaxillofacial reconstruction with varying efficiency in differentiation and proliferation.