The current article provides an overview on the application of capillary electrochromatography (CEC) to the analysis of body fluids. It takes into account works that have appeared in the literature since 1997 when the first paper was published on the topic. Major topics addressed are requirements for sample preparation, CEC separation conditions and detection techniques. Particular attention is focused on coupling CEC to mass spectrometry as a powerful tool for reliable analysis of complex matrices. The possibility of running real clinical samples is especially addressed since it can prove the suitability of CEC methods for biomedical analysis. Despite the rare acceptance of CEC as an analytical technique and the limited development of column technology, CEC can be used for analyzing toxics, drugs and related compounds in biological fluids, because it can combine several separation mechanisms.