Stem cell-based applications have become a popular and promising approach for therapy for a number of disorders including neurodegenerative diseases, degenerative muscle diseases, and osteoporosis, as well as trauma, inflammations, burns, and injuries. Human tooth germ stem cells are an adult stem cell source; they have mesenchymal stem cell properties and show high proliferative and differentiation capacity. Melatonin has been demonstrated to regulate differentiation of human and mouse mesenchymal stem cells into various cell lineages in addition to its other functions in the body. In the current study, the effects of melatonin on osteogenic, neurogenic, adipogenic, chondrogenic, myogenic, and odontogenic differentiation of human tooth germ stem cells were investigated. The results showed that melatonin increases the viability of cells. It significantly augments osteogenic, neurogenic, chondrogenic, myogenic, and odontogenic differentiation of the cells, whereas it reduces adipogenic differentiation capability. These results suggest that melatonin has a great potential to increase differentiation capacity of human tooth germ stem cells and might be useful in regenerative therapy applications involving stem cell differentiations in addition to defining potential treatments for obesity because of its suppressor effects on adipogenesis.