In this chapter a microchip-based electrochemical enzyme immunoassay is developed and its performance is demonstrated for the determination of monoclonal mouse IgG as a model analyte. Such a direct homogeneous immunoassay requires the integration of electrokinetic mixing of alkaline phosphatase (ALP)-labeled anti-mouse IgG antibody (Ab-E) with the mouse IgG antigen (Ag) analyte in a precolumn reaction chamber, injection of immunochemical products into the separation channel, followed by rapid electrophoretic separation of enzyme-labeled free antibody and enzyme-labeled antibody-antigen complex. The separation is followed by a postcolumn reaction of enzyme tracer with p-aminophenyl phosphate (p-APP) substrate (S) and downstream amperometric detection of p-aminophenol (p-AP) product. Factors influencing the reaction, injection, separation, and detection processes are optimized. We have characterized the microchip-based immunoassay protocol. The resulting attractive analytical performance, along with distinct miniaturization and portability advantages of the electrochemical microsystem, offer considerable promise for designing self-contained and disposable chips for decentralized clinical diagnostics.