Early screening and diagnosis of diseases require the development of sensitive, reliable, and inexpensive high-throughput assays. There is a growing need for innovative diagnostic technologies that provide accurate detection of a broad range of diseases and enhance laboratory productivity. Developments in micro-and nanotechnology have advanced the "lab-on-a-chip" concept towards a new generation of point-of-care diagnostic devices that enable parallel detection of multiple analytes in small-volume samples with high sensitivity in a short time. These features fulfill some of the important criteria of bioanalysis used for biochemical studies, environmental analyses, and clinical diagnostics. However, the multiplexing capability of microfluidic-based assay is limited compared to conventional flow cytometric assays, particularly for encoded microbead-based assays, which are capable of simultaneously analyzing multiple analyte. It is possible to incorporate the microbead-based assays into microfluidic devices in order to retain all the advantages of the microdevice and significantly improve multiplexing capability. In this chapter, we summarize the latest development in microbeadbased assays and discuss the integration of the microbead technology with microfluidic devices. Applications of the integrated approach in multiplexed protein and DNA analysis are growing rapidly in the areas of biomarker research, cancer screening, and disease diagnosis. The prospects for future development and commercialization of these microbead-based microfluidic devices are also discussed.