This review aims to highlight the current role of microchip CE (MCE) in clinical analysis to date, and also its future potential in this important area. One of the most notable advancements in separation science, which has accelerated in the last decade, has been the use of plastic and glass microchips to achieve high-speed electrophoresis separations in seconds, requiring only pico or nanolitre sample volumes. So far, in the clinical laboratory, MCE has lent itself to the resolution of very complex challenging analytes such as DNA, RNA, protein analysis, cellular components and other disease biomarkers. At present, most basic clinical laboratories rely heavily upon various kinds of enzymatic immunoassays as these methods offer speed, specificity, reliability and are well established analytical methods. However, this is not always the case, as with all analytical methods there are limitations, and sometimes enzymatic-based assays can be challenged by low-level concentration of target analytes present in samples resulting in high RSD values and results that cannot be interpreted. In some cases, this difficulty can be exasperated when complex sample matrices are presented for analysis, and interfering components result in highly exaggerated results from unwanted extra enzymatic binding. MCE may have a role in providing alternative highly sophisticated automated clinical analysis using state-of-the-art methodologies.