In many studies, adult stem cells have been found in human periodontal ligament (PDL), but in most cases they were found in the permanent teeth. The aim of the present study was to characterize stem cells from the PDL of deciduous teeth (dPDLSCs) and compare them with those from the PDL of permanent teeth (pPDLSCs). Stem cell markers were examined by a flow cytometric analysis. The results of in vitro differentiation into adipogenic and osteogenic lineages were analyzed by histochemical staining and quantitative reverse transcription-polymerase chain reaction (RT-PCR). The results of in vivo transplantation were analyzed by histological staining, immunohistochemical staining, and quantitative RT-PCR. There were no significant differences in the proliferation rate, cell cycle distribution, expressions of stem cell markers such as Stro-1 and CD146, or in vitro differentiation. The pPDLSC transplants made more typical cementum/PDL-like tissues and expressed more cementum/PDL-related genes (CP23 and collagen XII) than did the dPDLSC transplants. Together, these results suggest that pPDLSCs are better candidates for use in reconstructing periodontium.