The focus of this presentation is the development of optically barcoded silica beads for use in high-throughput, multiplexed screening applications such as protein microarrays or flow cytometry. Luminescent semiconductor core-shell, CdSe/ZnS QDs nanocrystals (or quantum dots (QDs)) with different emission wavelengths (colors), and encapsulated in different compositions in silica beads are used to define an optical barcode. Quantum dots are usually fabricated so they are stably dispersed in an organic solvent. This is accomplished by terminating the qdot surface (capping) with an tri-alkyl phoshine or a long chain amine. In order to facilitate the incorporation of the qdot into the hydrophilic silica environment it is necessary that the qdots are dispersible in water. We have achieved this first step by coating the qdots with polyvinyl-pyrolidine (PVP). Following this step, the water stable qdots are incorporated in a Stoeber approach that results in the encapsulation of the PVP coated qdots in polymerizing silica. Confocal laser scanning microscopy (CLSM) images of the nanocrystal luminescence in the bead interior indicate that the QDs are segregated into inclusions distributed throughout the bead. CLSM and fluorimetry measurements of the emission spectra of PS beads embedded with three color QDs in varying concentrations are reported which verify that distinguishable optical barcodes derived from the spectral scans of these QD can be obtained by this technique.