Magnetic nanoparticles have emerged as an important class of functional nanostructures with potential applications of magnetic resonance imaging, drug targeting, and bio-conjugation. We have developed a modified sol-gel approach to synthesize stable and well-dispersed magnetic Co@SiO2 nanoparticles with improved control over shell thickness and larger core diameters. These well-defined Co@SiO2 core-shell nanoparticles exhibit useful magnetic properties, and the protective silica shell allows them to be surface modified for bioconjugation for various biomedical applications. The core-shell nanoparticles were characterized by transmission electron microscopy, energy-dispersive spectroscopy, elemental mapping, and the line compositional analyses to demonstrate that uniform individually isolated core-shell nanoparticles are obtained through the improved synthetic route.