Multi-walled carbon nanotubes (MWNTs) were functionalized with poly(L-lysine)(PLL) and used to prepare the silica-MWNT nanocomposites via biomineralization route in the presence of PLL by a sol-gel reaction of tetramethyl orthosilicate. The MWNT-graft-PLL (MWNT-g-PLL) could be synthesized, and it was evidenced by FT-IR spectroscopy and TEM measurement. In TEM observation, the morphology of PLL molecules covered on MWNTs was clearly shown. The formation of silica on MWNT and MWNT-PLL was carried out in two methods called as solution phase and solid phase. The presence of PLL in biomineralization affected dominantly an amount of silica formed in both solution phase and solid phase, which was evidenced in the EDS image measurements.