The synthesis of magnetic, monodisperse nanoparticles has attracted great interest in nanoelectronics and nanomedicine. Here we report the fabrication of pure magnetite nanoparticles, less than ten nanometers in size, using the cage-shaped protein apoferritin (Fe(3)O(4)-ferritin). Crystallizable proteins were obtained through careful successive separation methods, including a magnetic chromatography that enabled the effective separation of proteins, including a Fe(3)O(4) nanoparticle (7.9 ± 0.8 nm), from empty ones. Macroscopic protein crystals allowed the fabrication of three-dimensional arrays of Fe(3)O(4) nanoparticles with interparticle gaps controlled by dehydration, decreasing their magnetic susceptibilities and increasing their blocking temperatures through enhanced dipole-dipole interactions.