Sol-gel procedures have been developed to encapsulate inorganic nanocrystals including metallic Au and II-VI semiconductor materials (CdSe/Cd(1-x)Zn(x)S) in SiO2 particles by using tetraethyl orthosilicate. The key strategy was the control of a sol-gel procedure. The anisotropic deposition of SiO2 monomers occurs because well-developed crystal facets having different affinity to SiO2 monomers. SiO2 monomers were not homogeneously deposited on nonspherical Au and CdSe/Cd(1-x)Zn(x)S nanocrystals. A surface silanization process, partly hydrolyzed tetraethyl orthosilicate were attached to the nanocrystals instead of initial ligands, plays an important role for the nanocrystals coated homogeneously with a SiO2 layer. Furthermore, CdSe/Cd(1-x)Zn(x)S nanocrystals were homogeneously coated with a thin SiO2 layer by the surface silanization process and a subsequent reverse micelle route. Colloidal Au nanocrystals were homogeneously coated with a SiO2 shell by the surface silanization process and subsequent Stöber synthesis without using a silane coupling agent or bulk polymer as the surface primer to render the Au surface vitreophilic. These results indicated partly hydrolyzed tetraethyl orthosilicate has an ability to replace the ligand on nanocrystals. After surface modification, the SiO2 particles with nanocrystals were conjugated with antibody for bioapplications.