A protocol for the qualitative and quantitative analysis of novel arginine-based cationic surfactants using HPLC and CE was studied and compared. The optimization of the analytical conditions was carried out through a systematic variation of the experimental parameters such as mobile phase, eluent conditions, ion pairing and amount of sample for HPLC, and type of buffer, ion strength, type and amount of organic solvent, sample injection time, applied voltage and column washing and conditioning for CE.