Quality control of active pharmaceutical ingredients (API) is commonly performed by means of HPLC. However, CE offers a suitable alternative, especially for the analysis of easily chargeable substances, i.e., amino acids. The article reviews, on the one hand, CE methods developed for impurity profiling of synthesized amino acid analogs. However, nowadays, production of amino acids/peptides is dominated by fermentation. Therefore, on the other hand, CE methods for the analysis of amino acids and small peptides are reported. The results of CE analysis of glutathione samples according to the monograph in the European Pharmacopoeia (Ph. Eur.) 5.7 and amino acid samples after derivatization with 9-fluorenylmethyl chloroformate (FMOC) and 3-(4-carboxybenzoyl) quinoline- 2 -carboxaldehyde (CBQCA) may pave the way for impurity profiling of fermentatively produced API by means of CE.