Objective: The aim of the present study is to isolate and characterize salivary gland stem cells and periodontal stem cells from adult albino rat. A comparison was carried out between their surface markers expression utilizing surface markers for flow cytometry. The odontogenic differentiation of salivary gland stem cells and periodontal ligament stem cells was assessed.Material and methods: Samples were collected from the two sources. PDLSCs and SGSCs were treated with collagenase before centrifugation to allow release of the cells. Cells were cultured in complete culture medium for 12-14 days. After reaching confluence, the isolated cells were characterized by flow cytometry using CD133 and C-Kit. The cells were induced for odontogenic differentiation by placing the cells in odontogenic induction media for 21 days. Odontogenic differentiation was evaluated by Alizarin Red stain and by the expression of Dentine Sialophosphoprotein (DSPP) which was assessed by RT-PCR.Results: The results showed that successful isolation of stem cells from periodontal ligament and salivary gland was achieved. Cells were successfully sub-cultured and expanded up to passage three. A flow cytometric analysis was done after stem cells isolation .PDLSCs were negatively expressed CD133 and C-Kit while SGSCs showed moderately positive expression of CD133 and C-KIT. The results showed that PDLSCs and SGSCs induced by odontogenic medium were stained by Alizarin Red at days 14 and 21. RT-PCR results indicated that all cultured cells efficiently differentiate into dentin forming cells and expressed specific DSPP gene which was expressed higher by PDLSCs than SGSCs in days 14 and 21.Conclusion: It can be concluded that PDLSCs show higher differentiation into odontogenic linage than SGSCs.