Cartilage tissue can be engineered by starting from a diversity of cell sources, including stem-cell based and primary cell-based platforms. Selecting an appropriate cell source for the process of cartilage tissue engineering or repair is critical and challenging, due to the variety of cell options available. in this study, cellular responses of isolated human chondrocytes, human embryonic stem cells and mesenchymal stem cells (MSCs) derived from three sources, human embryonic stem cells, bone marrow and adipose tissue, were assessed for chondrogenic potential in 3D culture. All cell sources were characterized by FACS analysis to compare expression of some surface markers. The cells were differentiated in two different biomaterial matrices, silk and chitosan scaffolds, in the presence and absence of bone morphogenetic protein 6 (BMP6), along with the standard chondrogenic differentiating factors. Embryonic stem cells-derived MSCs showed unique characteristics, with preserved chondrogenic phenotype in both scaffolds with regard to chondrogenesis, as determined by real time RT-PCR, histological and microscopical analyses. After 4 weeks of cultivation, embryonic stem cells-derived MSCs were promising for chondrogenesis, particularly in the silk scaffolds with BMP6. The results suggest that cell source differences are important to consider with regard to chondrogenic outcomes, and among the variables addressed here the human embryonic stem cells-derived MSCs were the preferred cell source. Copyright (C) 2009 John Wiley & Sons, Ltd.