A polydimethylsiloxane-glass capillary microchip is fabricated for the rapid analysis of a mixture of common biogenic amines using indirect fluorescence detection. Using a running buffer of phosphate and 2-propanol, and Rhodamine 110 as a background fluorophore, both co-ionic and counter-ionic systems are explored. Studies demonstrate the separation and analysis of cations using indirect fluorescence detection for the first time in a chip-based system. Resulting electrophoretic separations are achieved within a few tens of seconds with detection limits of approximately 6 lam. The reduced sample handling and rapid separations afforded by the coupling of indirect fluorescence detection with chip-based capillary electrophoresis provide a highly efficient method for the analysis and detection of molecules not possessing a chromophore or fluorophore. Furthermore, limits of detection are on a par with reported chip-based protocols that incorporate precolumn derivatisation with fluorescence detection. The current device circumvents lengthy sample preparation stages and therefore provides an attractive alternative technique for the analysis biogenic amines.