Silk protein and agarose are widely known as biocompatible materials in the human body. A three-dimensional (3D) scaffold composed of agarose and low-molecular- weight silk fibroin (LSF) was fabricated and examined in terms of structural characteristics and cellular responses in bone tissue engineering. This study showed that mouse pluripotent precursor cells attached to and proliferated uniformly on and within the LSF-containing 3D scaffold. Interestingly, cell proliferation and attachment was shown to be higher in a 3D scaffold containing 0.02% LSF, as compared to other LSF concentrations. The results of this study suggest that agarose-LSF scaffolds may be useful materials for tissue engineering.