This paper describes the analysis of biologically active amines by capillary electrophoresis (CE) in conjunction with laser-induced native fluorescence detection. In order to simultaneously analyze amines and acids as well as to achieve high sensitivity, 10 mm formic acid solutions (pH < 4.0) containing silica nanoparticles (SiNPs) were chosen as the background electrolytes. With increasing SiNP concentration, the migration times for seven analytes decrease as a result of increase in electroosmotic flow (EOF) and decrease in their electrophoretic mobilities against EOF A small EOF generated at pH 3.0 reveals adsorption of SiNPs on the deactivated capillary wall. The decreases in electrophoretic mobilities with increasing SiNP concentration up to 0.3 x indicate the interactions between the analytes and the SiNPs. Having a great sensitivity (the limits of detection at a signal-to-noise ratio (S/N) = 3 of 0.09 nm for tryptamine (TA)), high efficiency, and excellent reproducibility (less than 2.4% of the migration times), this developed method has been applied to the analysis of urinal samples with the concentrations of 0.50 +/- 0.02 mu m, 0.49 +/- 0.04 mu m, and 74 +/- 2 mu m for TA, 5-hydroxytryptamine, and tryptophan, respectively. The successful examples demonstrated in this study open up a possibility of using functional nanoparticles for the separation of different analytes by CE.