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This study aimed to compare the expression of "classical" stem cell markers, the proliferative capacity and differentiation ability of clonal mesenchymal stem cell (MSC) populations isolated from animal matched dental pulp (DP) and bone marrow (BM) of rats. MSCs were derived from the aforementioned tissues, with immature MSCs selected for by preferential fibronectin-adherence and resultant single-cell derived clonal populations culture expanded. Colony forming efficiencies were 12 times greater for DP clones compared with BM clones. Expansion of isolated colonies, however, was 5 times more successful for BM clones. All clones exceeded 40 population doublings (PDs) and all exhibited periods of high and low proliferative rates. PDs were approximately 1.5 times higher for BM clones. All BM clones readily differentiated towards osteoblasts, chondrocytes and adipocytes. Of the three DP clones analysed, all demonstrated osteogenesis, albeit with reduced efficiency compared to BM clones. One clone demonstrated adipogenesis and one clone chodrogenesis. qPCR determined quantifiable differences in Msx2, Vcam2 and Mcam with no clone showing similarity to another. The expression of a specific mesenchymal marker did not predict proliferative or differentiation potential. These results also suggest lineage restriction of the DP clones.