Quantum dots (QD) of a CdSe-ZnS core-shell structure are coated with silica spheres to improve their stability in biological buffers and biocompatibility in fluorescence imaging. We found that it was critical to transfer quantum dots from organic phase to aqueous phase before the silica shell growth process. As a result, high quality CdSe-ZnS-SiO2 core-shell-shell nanoparticles were prepared in high yields and their size and distribution are characterized with transmission electron microscopy and dynamic light scattering, which yielded uniform sizes and narrow polydispersity. Single particle fluorescence spectroscopy on the silica-protected quantum dots showed they were stronger emitters with consistent fluorescence intensity and "on-off" behaviors than bare CdSe-ZnS nanocrystals.