In this dissertation, microfluidic systems that integrate antibody-based sample preparation methods with electrophoretic separation are developed to analyze multiple biomarkers in a point-of-care setting. To form an affinity column, both monolith materials and wall-coated channels were explored. I successfully demonstrated that monolith columns can be prepared in microfluidic devices via photopolymerization. The selectivity of monolith columns was improved by immobilizing antibodies on the surface. These affinity columns can selectively enrich target analytes and reduce the signal of contaminant proteins up to 25,000 fold after immunoaffinity extraction. These results clearly demonstrate that microchip affinity monoliths can selectively concentrate and purify target analytes through specific antibody-antigen interactions. These monolith columns operated well for simple systems such as buffered solution, but suffered from clogging with real biological samples such as human serum. Therefore, I developed new affinity columns using a wall coating protocol. To form the affinity columns, a thin film of a reactive polymer was UV polymerized in a microchannel. Antibodies were attached by reaction between the polymer epoxy groups and antibody amine groups. All steps, including loading, washing, and elution for affinity extraction, as well as capillary electrophoresis analysis, were achieved simply via applying voltages to reservoirs on the microdevice. By adding reservoirs containing alpha-fetoprotein (AFP) standard into the same device, a quantitative method, either standard addition or calibration curve, can also be performed on-chip. These polymer microdevices have been applied in determining AFP levels in spiked serum samples, and the results are comparable with the values measured using a commercial enzyme linked immunosorbent assay kit. These microchips have also been adapted for detection of multiple biomarkers by immobilizing different antibodies on the affinity column. Four kinds of antibodies were attached to microchip columns, and the amounts of immobilized antibodies were characterized. The fluorescence signals of all four protein antigens were in the same range after rinsing, indicating that the derivatization reaction had little bias toward any of the four antibodies. With spiked human blood serum samples, four proteins in the ng/mL range were simultaneously quantified using both calibration curves and standard addition. In general, the calibration curve and standard addition results were close to the known spiked concentrations. These results indicate that my integrated microdevices can selectively retain and analyze targeted compounds in clinical samples. Moreover, my platform is generalizable and applicable for the simultaneous quantification of multiple biomarkers in complex matrices.