Capillary electrophoresis has garnered for the analysis of clinically relevant molecules. As a result of its potential for rapid development of high speed, high efficiency electrophoretic separations under native or denaturing conditions, capillary electrophoresis has found its way into many sectors of the clinical diagnostic laboratory. As a cost-effective, automated technology, it avoids the costly chromatographic columns associated with HPLC and the labor-intensive methodologies of conventional gel electrophoretic techniques. This overview discusses the versatile nature of this technique for the analysis of a variety of clinically-relevant analytes ranging in size and character. This will be illustrated with specific examples of the use of CE for the detection of drugs, proteins and DNA associated with the diagnosis of a variety of disease states. The limitations of CE with testing involving high sample throughput will be addressed in the context of the next generation of capillary electrophoresis systems, electrophoretic analyses on microfabricated chips.