The focus of this presentation is the development of optically bar-coded beads that would be used in an ultra-miniaturized protein or chemical micro-array platform for multiplexed screening applications. This platform consists of optically encoded, 1 micron diameter polystyrene beads which are arrayed in a square grid on a substrate. This array is prepared in the following way: A surface consisting of microwells of diameter and depth of the order of the beads is first fabricated using photolithography on silicon wafers. The interior of the wells is functionalized with self assembling monolayers (SAMs) with pendant groups designed to bind a single bead to the inside of each well. The area on the substrate surrounding the wells is chemically functionalized with a polyethylene glycol terminated SAM to resist nonspecific adsorption in screening assays. The beads are optically encoded using a barcode consisting of fluorescing, hydrophobically modified semiconductor nanocrystals (quantum dots (QDs) embedded within the beads. QDs with different emission wavelengths (colors) and encapsulated in different concentrations inside the beads are used to define a code based on intensity (i) and color (c). The encapsulation is undertaken by copolymerizing the PS beads with the QDs using a suspension polymerization procedure. The mechanism is detailed by which these QDs are incorporated in the PS matrix allowing for a controlled distribution of colors and compositions. The array is assembled by first preparing aliquots of beads, with each aliquot consisting of beads with the same QD barcode, mixing aliquots together and finally depositing the bead mixture onto the microwell grid surface. Results are reported for a prototype study consisting of a few colors and intensity levels using CdSe/ZnS core-shell semiconductor nanocrystals. Scanning electron microscopy and particle size analysis is used to confirm the one micron size of the PS beads with encapsulated QDs. Atomic force and fluorescence microscopy are used to demonstrate that each well is occupied by a single bead. Confocal laser scanning microscopy is used to demonstrate the uniform distribution of the QDs in the beads, and the ability to read the barcodes in a distinct manner at each registry position. This array of optically encoded beads is designed to be used as a protein or chemical microarray. Probe molecules are bound to the bead surfaces (with each probe identified with a QD bar code) and screened against targets present in a solution deposited as a microliter drop on the array surface. Binding of a target to a probe is detected usually 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. This design has several advantages over conventional protein and chemical arrays. The micron-scale of the beads and the grid allows a registry density of 10^5, which is orders of magnitude larger than the density of conventional arrays consisting of dried spots of probe molecules with each spot of the order of approximately 100 microns. The encoding capacity of the QDs (i^c) allows for the bar coding of this large number of registries. 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.