Abstract Aim Different tissues of dental origin are used for isolation of stem cells that can be differentiated towards osteogenic or odontogenic lineages, including dental follicle and apical papilla. Using tooth germ as a whole without separating dental follicle and apical papilla for isolating stem cells is another approach that uses the reciprocal interactions between two cell types. Although dental follicle stem cells and stem cells form apical papilla are widely investigated for both osteogenic and odontogenic differentiation, use of tooth germ stem cells is very limited despite its potential. This study aimed to investigate and compare the osteo/odontogenic differentiation potential of stem cells from apical papilla, tooth germ, and dental follicle in vitro. Methods Dental stem cells isolated from porcine were assessed in terms of cell surface antigens, multilineage differentiation, and cell proliferation. Osteo/odontogenic response was assessed with alkaline phosphatase activity, calcium deposition, von Kossa staining, confocal microscopy, and the expression of osteo/odontogenic markers by real‐time PCR at Days 7, 14, and 21. Results All cell types showed expression of mesenchymal stem cell markers and differentiated towards chondrogenic and osteogenic lineages, while adipogenic differentiation was weak. Stem cells from apical papilla responded to osteo/odontogenic differentiation faster than that of dental follicle and tooth germ stem cells, but all groups indicated formation of mineralization and expressed osteogenic gene markers. Conclusion All three cell types displayed similar biological characteristics and are appropriate candidates for bone regeneration.