Teeth are a significant source of stem cells and have clinical importance for regenerative medicine. A human tooth harbors different kinds of stem cells in the dental pulp (DPSC) or the periodontal ligament (PDLSC). Also exfoliated teeth in childhood contain a special type of stem cells in their pulp called Stem cells from Human Exfoliated Deciduous teeth (SHED). All these stem cells have features and capacities that vary depending on their niche. Here we investigated the proteomic properties of three types of stem cells that originated from human teeth. We isolated and cultured the DPSCs, PDLSCs, and SHED cells. After validating MSC populations via immunophenotyping, we performed a mass spectrometry-based proteomic approach to identify and relatively quantify whole cell and secreted proteins. Identified proteins were evaluated by using Gene Ontology and Reactome pathway analysis tools. Our data reveal that SHED cells represented inflammation, hypoxia, and nutrient deficiency-associated ontologies in both their secretome and whole-cell proteomes. The whole-cell proteome of PDLSCs consisted of differentiation and proliferation-associated molecules while their secretory molecules were mainly associated with inflammation, ECM organization, and immune response. Among dental-originated stem cells, DPSCs appeared to be the healthiest and clinically relevant in terms of proteomic properties with their proliferation, growth factor signaling, and stemness-associated molecules in their secretome and whole-cell proteome. Obtained results demonstrated that every type of stem cell from dental origin has unique proteomic features that are altered by their location and physiological conditions. The findings may help researchers improve the dental stem-cell-based regenerative medicine approaches.