In the field of tissue engineering for bone regeneration, there have been many studies that examined in the bone forming ability of the porous biomaterials with mesenchymal stem cells (MSCs). To promote the tissue engineering approach in clinical situation, there is a need for the establishment and standardization of evaluation methods for measuring the in vivo bone forming ability. In this study, we examined the seeding process using rat MSCs to ascertain whether it is a valid protocol for various materials. Our results showed that the cell seeding process for the fabrication method of MSCs/materials composite influenced the number and distribution of the MSCs in the materials, therefore the process is a key to show new bone formation which derived from the seeded MSCs. Here, we describe the detailed process which can show consistent new bone formation in pores of the materials.