Successful therapy for radiation-induced salivary gland (SG) hypofunction is currently unavailable; however, tissue-specific stem cells are expected to be promising candidates for SG regeneration. Here, we present our method for the establishment of single cell-derived clonal stem cells from mouse SGs and describe their characteristics. Salivary gland-derived clonal stem cells (SGSCs) were isolated and expanded in vitro by a modified subfractionation culture method. The properties of SGSCs were examined with respect to their marker expression, gene expression, differentiation potential, and in vitro immunosuppressive activity relative to bone marrow-derived mesenchymal stem cells (BM-MSCs). SGSCs appeared to largely share the characteristics of BM-MSCs based on their marker expression, whereas they differentially expressed some genes, including AQP5, E-Cadherin, Laminin, ZO-1, and COL4. SGSCs showed the ability to differentiate into fat, bone, and cartilage cell types, as well as into α-amylase-producing and hepatocyte-like cells after appropriate induction. The in vitro immunosuppressive activity of SGSCs was found to be more potent than that of BM-MSCs. These results showed that SGSCs possess the properties of MSCs with some differential gene expression and they are salivary-specific stem cells with both epithelial and mesenchymal properties. The biological functions of SGSCs and their relevance to SG epithelial progenitor cells require further investigation.