It has been established that human dental pulp and periodontal ligament contain a population of mesenchymal stem cells (MSCs). However, the phenotypic analysis in terms of putative stem cell markers expressed by these stem cell populations is incomplete. It is relevant to understand whether stem cells derived from closely related tissues are programmed differently. This book therefore, provides an insight into the phenotypes of dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PDLSCs). Both the stem cells express embryonic stem (ES) cell markers. Differences were observed in expression of stemness-related markers. DPSCs displayed increased percentages of SSEA4, CD13 and CD166 and decreased CD9 expression compared to PDLSCs. Both stem cells express common MSC markers, different levels of expression suggests there might be more than one stem cell population existing within these tissues which differ in their embryonic status, and DPSCs are a more primitive stem cell population in comparison to PDLSCs. This analysis should shed some light into the nature of stem cells from dental tissues and help researchers utilize these stem cells for regenerative medicine.