Silanization is a convenient route to provide water-solubility to the quantum dots (QDs) with different structure. Green, orange and red emitting CdSe-based QDs were synthesized by varying of number and material of wider-band gap shells and fluorescent properties of QDs were characterized before and after silanization. It was shown that structure of the QD influences on the quantum yield of the silanized QDs: the better CdSe core is protected with wider-band gap semiconductor shells, the more fluorescence properties remain after silica coated QD possess. Hence silica coated QDs have a great perspectives for the multiplex analysis