Recently the creation of calcium compounds with a highly controlled ultrastructure is noted as next generation materials for biomedical applications. Here we propose the novel method for synthsizing calcium nanoparticles using iron strange protein, apoferritin. Apoferritin was incubated in saturated Ca(HCO3)2 solution at 18 °C. Temperature of the reaction solution was then increased to 37 °C and left for 2 hours to make CaCO3 sedimentated. After removing the sediments in the bulk solution by centrifugation, the supernatant was concentrated. Saturated Ca(HCO3)2 was added to it and the mixed solution was incubated at 37 °C for 30 min. This process was repeated four times. With a Transmission Electron Microscope (TEM), nearly spherical particles with a diameter of about 6 nm were observed to form in the cavity of apoferritin. The nanoparticles were observed to have a lattice structure of spacing about 0.22 nm with high resolution TEM. With Energy Dispersive X-ray spectroscopy (EDS) analysis, the peak of Ca (Kα; 3.7 keV) was detected from a synthesized nanoparticle. According to the solvent condition, nanoparticles formed in the apoferritin cavity would be CaCO3.