The Hadamard transform (HT) technique, which permits the S/N in CE to be improved, was applied to MEKC. Multiple sample injection of fluorescent analytes according to a Hadamard code sequence was performed using an optically gated sample injection technique, in which a sample plug was produced based on photodegradation by irradiation with an intense laser beam. The capillary and reservoirs were filled with a sample solution containing buffer components and SDS as a pseudostationary phase. A preliminary study confirmed that fluorescein ion could be photobleached in the presence of SIDS. The optically gated sample injection technique was then applied to multiple sample injection, based on a Hadamard matrix. The S/N in the electropherogram obtained by HT-MEKC was improved substantially compared to that obtained by a single injection method. When the technique was applied to the separation of several amino acids labeled with FITC, the S/N ratio for each amino acid was enhanced, without any evidence of degradation in separation resolution. Moreover, HT-MEKC was applied to the analysis of amino acids contained in a Japanese beverage, resulting in improved S/Ns for the amino acids.