Mixtures of nitroaromatic and nitramine explosive compounds and their degradation products were analyzed using electrokinetically driven separations with both indirect laser-induced fluorescence (IDLIF) and UV absorption detection. Complete separations of the 14-component mixture (EPA 8330) were achieved using both capillary electrochromatography (CEC) and micellar electrokinetic chromatography (MEKC). IDLIF detection was performed using an epifluorescence system with excitation provided by a 635 nm diode laser and micromolar concentrations of the dye Cy-5 as the visualizing agent. While the sensitivity of the two detection methods was similar for the nitroaromatic compounds, the nitramines could only be detected using UV absorption due to their low fluorescence quenching efficiency of Cy-5. The detection sensitivity using IDLIF was limited by low frequency oscillations in the fluorescence background. The oscillations increased with higher electric field strength and were attributed to thermal fluctuations caused by Joule heating. Due to the more conductive running buffer and higher separation currents used in MEKC, sensitive IDLIF detection could only be achieved using low (similar to 100 V/cm) field strengths, resulting in long analysis times. CEC separations, which are typically run with low conductivity mobile phases to avoid bubble formation, are less sensitive to this effect. In CEC separations with IDLIF detection a stable fluorescence background using Cy-5 could be established using only a nonporous stationary phase. In capillaries packed with porous silica particles, anomalous migration behavior was observed with charged dye molecules and a stable fluorescence background could not be established under electrokinetic flow. This is the first demonstration of IDLIF in packed channel CEC.