Periodontal ligament (PDL) is capable of regenerating several types of periodontal tissues. However, the stem cells in PDL have been less well characterized. Recently, it has been represented that stem cells have a potent ability to exclude Hoechst dye, and cells possessing this phenotype are termed "side population (SP)." In addition, it is suggested that the SP cells are ubiquitously present in adult tissues, therefore, we investigated the presence of SP cells in PDL. Hoechst dye efflux assay showed that PDL cells include 3.9% SP cells. This SP profile disappeared in the presence of verapamil or reserpine. Only ABCG2-expressing cells were detected in PDL cells by flow cytometric analysis. Furthermore, RT-PCR demonstrated that ABCG2 mRNA expression remarkably correlated with PDL SP phenotype. Our findings demonstrate that PDL contains ABCG2-dependent SP cells. Hence, it is possible that this population could contribute to periodontal tissue regeneration as PDL stem cells.