During the past decade, capillary electrophoresis (CE) emerged as a promising, effective and economic approach for separation of a large variety of substances, including those encountered in clinical and forensic analysis. Reliable and automated CE instruments became commercially available and promoted the exploration of an increasing number of CE methods and fields of application. The widespread applicability of CE, its enormous separation power and high-sensitivity detection schemes make this technology an attractive and promising tool. This review discusses the principles and important aspects of CE-based assays and provides an overview of the key achievements encountered with CE in clinical and forensic analysis, including those associated with the analysis of serum proteins, hemoglobin variants, drugs and nucleic acids. Validated assays, interesting applications and future trends in clinical and forensic analysis are also discussed.