This review treats the coupling of capillary electrophoresis (CE) with fluorescence detection (Flu) for the analysis of natively fluorescent biomolecular and pharmaceutical compounds. CE-Flu combines the excellent separation efficiency of CE with the high selectivity and sensitivity of Flu. In CE-Flu, an appropriate design of the fluorescence detection cell is very important in order to achieve efficient analyte excitation in and emission light collection from the small cylindrically-shaped detection volume. Therefore, due attention is paid to the various optical detection designs used for CE-Flu, including the applied excitation sources and emission light detectors. Special attention is devoted to wavelength-resolved Flu and to sensitivity issues. Furthermore, he specific requirements for fluorescence detection in microfluidic systems (i.e. chip-based electrophoresis) are discussed. Subsequently, an overview of described applications of CE-Flu for the analysis of natively fluorescent biomolecules and drugs is presented in extensive tables, treating amino acids, peptides, proteins, bioactive compounds, flavins, pharmaceuticals and also single cell analysis. The tables provide information on analyte nature, sample matrix, optical detection aspects, CE mode and limits of detection. A selection of descriptive applications is discussed in detail to illustrate the potential of native fluorescence detection in CE. It is concluded that CE-Flu is a powerful tool for biomolecular and pharmaceutical analysis, and provides good opportunities for use in lab-on-chip devices. © 2012 Elsevier B.V.