CdSe nanoparticles were synthesized in the cavity of the cage-shaped protein, apoferritin, by designing the slow chemical reaction system of Cd2+ and Se2-. The cavity size of apoferritin molecules is around 7 nm and the diameter of synthesized CdSe nanoparticles is about 6 nm with small size dispersion. CdSe nanoparticles as prepared are multi-crystalline and can be made into a single crystal by the heat-treatment under nitrogen gas. This bio-template synthesis provides a new method to synthesize uniform CdSe nanoparticles.