Two prototypes of microstructured capillaries (MSCs) were designed, manufactured, and used to carry out different experiments. MSC-1 consisted of six holes of approximate to 28m id whereas MSC-2 consisted of 85 holes of approximate to 7.7m id. A fundamental study on the hydrodynamic injection through a commercial CE equipment was conducted. Experimental times to flush specific volumes were approximately three times larger than the theoretical values. Then, the detection of starch was carried out by using the MSCs and conventional capillaries, and the electropherograms were compared on the basis of analytical parameters employed in CE. An improvement in peak asymmetry was obtained for the MSC-1 compared to the conventional capillaries. S/N was one order of magnitude increased with the MSC, improving ten times the sensitivity. Considering this advantage, the separation and detection of nitrostarch was performed as a first application of the MSC-1. Minimal sample amounts of nitrostarch (1.7g) were detected. Results present a real interest in forensics since this substance had not been previously detected through CE, leading to new investigations in the design of new capillaries capable of enhancing CE performance.