Mesenchymal stem cells (MSCs) can regenerate missing tissues and treat diseases. Hence, the current work aimed to compare the proliferation rate and the osteogenic differentiation potential of bone marrow MSCs (BMSCs), gingival MSCs (GMSCs) and submandibular MSCs (SMSCs). MSCs derived from bone marrow, gingiva and submandibular salivary gland were isolated and cultured from rats. The proliferation capacity was judged by MTT proliferation Assay. Osteogenic differentiation was assessed by Alzarin red stain and quantitative RT-PCR was performed for Runx-2 and MMP-13. The highest significant proliferation was estimated in the BMSCs compared to GMSCs and SMSCs (p-value was < 0.01). All studied cell types formed mineralized nodules as stained with Alizarin Red stain at the 3rd passage of differentiation. However, BMSCs seemed to generate the highest level of mineralization compared to GMSCs and SMSCs. RT-PCR revealed that the expression of Runx-2 and MMP-13 mRNAs was significantly increased in the BMSCs compared to GMSCs and SMSCs (p-value was < 0.01). BMSCs displayed maximum osteogenesis results followed by the GMSCs and lastly by the SGSCs. Thus, it could be recommended that GMSCs can be used as a second choice after BMSCs when bone tissue reconstruction is needed.