The aim of this study was to develop a general approach for characterizing the impurity profile of amino acids at level 0.1% by means of capillary electrophoresis (CE). Checking a variety of labeling reagents revealed 9-fluorenylmethyl chloroformate to be favorable, due to the high stability of its derivatives and the fact that the reagent peaks do not interfere with the peaks of the impurities. After optimization, the method was sufficiently sensitive to evaluate impurities at a 0.1% level by UV detection. The method was representatively validated for phenylalanine (Phe) with regard to selectivity, precision, linearity and accuracy using model mixtures of potential impurities. The CE analyzes method was applied to Phe samples of different manufacturers and the capabilities of the strategy was also demonstrated by samples of tryptophan and serine.