This paper describes a system for integration of a one-step-microscale chemical derivatization and analysis by a methodology known as electrophoretically mediated microanalysis (EMMA). Differential electrophoretic mobility between an analyte, reagent, and their product offers EMMA a unique capability to selectively carry out electrophoretic mixing, control product formation, and separation. This system was successfully applied to perform derivatization and separation of the multicomponent aminoglycoside antibiotic gentamicin using 1,2-phthalic dicarboxaldehyde and mercaptoacetic acid as labeling reagents. A multivariate approach based on central composite experimental design was used to optimize the derivative yield. Full automation of the derivatization and analytical procedure, high derivatization efficiency, high sample throughput, and precision are the excellent features of the present method. In addition, this methodology offers short analysis time, as well as selectivity and sensitivity suitable for impurities determination. Separation of gentamicin C1, C1a, C2, C2a, C2b, sisomicin, and several minor components was achieved. For the first time separation and identification of three impurities, namely garamine, 2-deoxystreptamine, and paromamine are described.