The use of non-invasive methods for detecting biomarkers opens a new era in patient care, since clinical investigators have long been searching for accurate and reproducible measurements of putative biomarkers. There are many factors which make this research challenging, beginning with lack of standardization of sample collection and continuing through the entire analytical procedure. Among the variety of methods so far used for biomarker screening, capillary electrophoresis represents a robust, reliable, and widely used analytical tool. This review will focus on recent applications of CE to the analysis of body fluids and tissues for identification of biomarkers.