This study investigates the effect of scaffolds prepared from gelatin (G) and chitooligosaccharide (COS) on the osteogenic differentiation of rat bone-marrow-derived mesenchymal stem cells (MSC). The sponge scaffolds at G/COS mixing ratios of 100:0, 70:30 and 50:50 were fabricated by freeze-drying, followed by glutaraldehyde cross-linking. The pore size of the G/COS scaffolds ranged from 70 to 105 μm. MSC cultured in the scaffolds in the osteogenic medium were differentiated into osteogenic cells for all G/COS scaffolds. Calcium nodules were homogeneously formed on the surface of scaffolds cultured with MSC. A Fourier transform infrared (FT-IR) analysis demonstrated the formation of hydroxyapatite spectroscopically. Among all G/COS scaffolds, the highest ALP activity and calcium content were observed for MSC cultured in the G/COS 70:30 scaffolds. The G/COS 70:30 scaffolds were then pre-cultured with MSC in the osteogenic medium for 28 days and subcutaneously implanted into nude mice to evaluate ectopic bone formation. Enhanced vascularization, cell infiltration, collagen formation and calcium deposition around the scaffolds implanted were histologically observed at 2 and 8 weeks after implantation. It was concluded that the G/COS scaffold with the mixing ratio of 70:30 was a promising organic material to induce osteogenic differentiation of MSC.