A novel collagen sponge that can protect cell leakage during cell seeding was developed by wrapping all the surfaces except the upside of a collagen sponge with membrane that has pores smaller than cell. The collagen sponge was used for three-dimensional culture of human bone marrow-derived mesenchymal stem cells (MSCs). The cells adhered to the collagen, and proliferated to fill the spaces in the sponge. The cell seeding efficiency was higher than 95%. The MSCs cultured in the collagen sponge in the chondrogenic induction medium supplemented with TGF-β3 and BMP6 expressed genes encoding type II collagen, SOX9 and aggrecan. HE staining indicated the round morphology of differentiated cells and the extracelluler matrices were positively stained by safranin O and toluidine blue. Type II collagen and cartilage proteoglycan were detected by immunostaining with anti-type II collagen and anti-cartilage proteoglycan. These results suggest the chondrogenic differentiation of MSCs. The collagen sponge facilitated cell seeding and chondrogenic differentiation of MSCs, and will be useful for cartilage tissue engineering.