The focus of this presentation is the development of optically barcoded polymer beads for use in high-throughput, multiplexed screening applications such as protein microarrays or flow cytometry. Luminescent semiconductor nanocrystals (or quantum dots (QDs)) with different emission wavelengths (colors), and encapsulated in different compositions in polystyrene (PS) beads are used to define an optical barcode. The encapsulation is undertaken by copolymerizing the PS beads with hydrophobically capped, core-shell, CdSe/ZnS QDs, using a spraying suspension polymerization procedure. Liquid styrene monomer, containing a thermally activated free radical initiator and dispersed QDs in a prescribed composition, is sprayed as microdroplets (10-100 microns in diameter) into an aqueous solution. The microdroplets are then polymerized by heating, and the beads subsequently recovered. 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. The emission spectra also indicate Forster Resonance Energy Transfer (FRET) from the lower wavelength to the higher wavelength emitting QDs, providing evidence that the QDs are situated within nanometers of each other in the inclusions. The addition of non-luminescent nanocrystals, such as silica or iron oxide, along with the QDs to separate the QDs from one another in the inclusions and reduce the energy transfer is also reported. We also report the assembly of the encoded beads onto a substrate surface as a microarray. Beads with an encapsulated iron oxide nanoparticle are spread into a monolayer on a substrate surface, and a magnetic field is applied underneath the surface to affix the microbeads to the substrate. The surface has been previously passivated with a polyethylene glycol oligomer to prevent nonspecific adsorption of biomolecules in an assay. This assembly is a prototype to host biological probes such as peptides, and antibodies. (In addition, by coating the beads with bilayers and sequestering membrane receptors in the bilayers, this platform can be used for the display of difficult to present membrane receptors which require a lipid environment to retain their biological binding ability.) In the bead-formatted microarray, binding of a target to a probe is detected in the usual manner for microarrays by the luminescence of a fluorescent label on the target. By reading the code on the bead lit by this label, the identity of the probe molecule binding the target can be obtained. The microbead array platform investigated in this study has several advantages over conventional protein and chemical arrays, which are formed by spotting probe molecules down onto a surface. The micron-scale of the beads and the grid allows a probe density, which is orders of magnitude larger than the density of conventional microarrays fabricated by fluid spotting. In addition, the high encoding capacity of the QDs allows for the bar coding of this large number of probes.