We have set up and evaluated a microchip capillary electrophoresis (CE) laboratory experiment for the instrumental analysis laboratory class at Brigham Young University (BYU). In this experiment the students learn to load liquids into microfluidic channels, to align polymer microchips in a laser-induced fluorescence (LIF) detection microscope, and to perform microchip CE of fluorescently tagged amino acids. Moreover, the students study how the injection time duration and distance to detection in a CE microchip affect the separation. In this manuscript, we describe what is needed to set up and carry out this laboratory. In addition, we discuss the experimental outcomes from various student groups who have completed this experiment. This new laboratory module provides students with valuable training in the fields of microfluidics and separations, and should help the next generation of chemists learn to use microscale methods.