Clinical chemistry also known as chemical pathology is a discipline that is generally concerned with analysis of biological fluids for diagnosis of human diseases. Capillary electrophoresis (CE) is electrophoretic separation run in narrow‐bore capillary format, which has become a highly efficient and versatile separation technique available for analysis of a wide variety of biologically active molecules. Implementation of CE in clinical laboratories will enhance the capability of the current clinical diagnostic system and improve the efficiency and quality of routine clinical testing. Owing to the nature of clinical diagnostics, the adoption of CE in clinical laboratories has been slow. However, CE has begun to replace some older and antiquated conventional techniques with unique applications in some pioneering clinical laboratories. This review covers a brief introduction to the CE technique (i.e. principle of separation, modes of operation, instrumentation, and practical considerations), and a summary of its applications in clinical chemistry (i.e. proteins, nucleic acids, drugs, and organic and inorganic ions), as well as the future prospects of this field.