In the present study, we have demonstrated that alginate and collagen sponge can act as scaffolds in order to support 3-dimensional structure for the differentiated bone marrow derived mesenchymal stem cells (BMSCs) during chondrogenesis in vitro and in vivo. The chondrogenic induced BMSCs were well distributed and differentiation in scaffolds system before implantation, then they produced sufficient ECM in the implants to form chondroid aggregates in vivo. In our opinion, well-differentiated BMSCs is a crucial feature of cartilage repair and only can be achieved in scaffold matrix. Furthermore, when dealing with cartilage defects, alginate seem to be superior to collagen sponge, and the combinational strategy of pre-induced BMSCs combined with alginate 3D-culture might be useful in improving conventional autologous cells transplantation or free-cells scaffolds.