To develop a new co-culture system, the separable-close co-culture system, to replace the indirect co-culture system which analyzes cellular interactions between two groups of cells with each type being cultured separately and also the direct co-culture system where the two cell types are cultured together. The new system not only achieved effective cellular interactions but also allowed the effect that one group of cells has on another group of cells to be evaluated. We performed co-culturing of human bone marrow mesenchymal stem cells and human articular chondrocytes using the new system. The new system made it possible to assess separately the effects of one group of cells on the other cell type, as in the indirect co-culture system. Furthermore, the new system rivaled or surpassed other co-culture systems in terms of the chondrogenic gene expression. The new co-culture system is effective in terms of assessing gene expression in two cell types.