Mesenchymal stem cells (MSCs) from a variety of mesenchymal tissue contain common features, but distinguishing properties dependent on their origin are emerging. We investigated morphological differences of human bone marrowMSCs, synovium-MSCs, and chondrocytes during in vitro chondrogenesis. Two hundred thousands cells were pelleted after centrifugation and cultured in chondrogenic media that contained BMP-2, TGF-b3, and dexamethasone. The pellets were analyzed histologically, immunohistologically, and electron microscopically. Before chondrogenic induction, trypsinized MSCs and chondrocytes looked similar. At day 1, the structure of the three masses was divided into two layers, and the most obvious differences in the three populations were observed in the deep zone. In bone marrow-MSCs, round cells accumulated without intercellular space, and the cells were mainly connected through intermediate junctions. In synovium-MSCs, elongated cells accumulated with small desmosomes and intercellular spaces could occasionally be seen. In chondrocytes, separated oval and polygonal cells connected only in a narrow spotty area through a small desmosome. At day 7, the structure of the three masses was divided into three layers, and the most obvious differences in the three populations were observed in the middle zone. In bone marrow-MSCs, the middle zone consisted of dense smaller cells and apoptotic cells. In synovium-MSCs, the middle zone consisted of dense arrayed wider cells and apoptotic cells. In chondrocytes, the middle zone was acellular without apoptotic cells. At day 21, the morphology of cells and extracellular space became similar in that each cell was located separately with abundant extracellular matrix. The superficial zone was still obvious in bone marrow-MSCs, but hardly seen both in synovium-MSCs and chondrocytes. In this study, we revealed morphological differences of bone marrow-MSCs, synovium-MSCs, and chondrocytes during in vitro chondrogenesis. The most obvious differences in the three populations were observed at day 1 in the deep zone.