Stem cell markers are utilized to isolate or identify stem cells. So far, many stem-cell-specific markers have been described, although some of them turned out to be not as specific as it was originally proposed. In this study, we sought to search for a specific stem cell marker that would be phenotypically helpful, characteristically specific, economically affordable and easy to use. Because organelles are one of the major characteristics of eukaryotic cells, we asked the question of whether organelle characteristics might be a useful tool for stem cell characterization. We studied distribution and characteristics of the endoplasmic reticulum, the mitochondria and the Golgi apparatus in human dental-pulp-derived mesenchymal stem cells before and during osteogenic differentiation. Although it was not possible to find a useful macromolecular marker for stem cell characterization, we found that during osteogenic differentiation, the stem cells changed their Golgi characteristics and displayed a unique in vivo pattern. We analysed these unique Golgi structures and proposed a potential osteogenic differentiation marker for human dental-pulp-derived mesenchymal stem cells. This pattern may be used in the evaluation of osteogenic differentiation. Copyright (C) 2011 John Wiley & Sons, Ltd.