Focus of this paper is the development of optically barcoded polymer beads for use in high throughput multiplexed screening applications such as protein microarrays. 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 the QDs using a spraying suspension polymerization procedure. A mechanism is detailed by which these QDs are incorporated in the bead matrix allowing for a controlled distribution of colors and compositions. QD embedded PS beads of approximately 50 microns in diameter are obtained. Confocal laser scanning microscopy (CLSM) and fluorometry results for the PS beads embedded with three color CdSe/ZnS core-shell QDs in varying concentrations are reported. Distinguishable optical barcodes derived from the spectral scans of these QD loaded PS beads are reported. These optically bar-coded PS beads arrayed in a square grid of microwells on a substrate will play host for biological receptors such as cell surface membrane proteins, whose interactions with target molecules in analyte solutions would be detected in high-throughput screening of drug molecules or pathogens.