Recently capillary electrophoresis (CE) has been used for the separation and detection of toxic heterocyclic aromatic amines (HAA) that are present in several environmental samples and food samples. Methods found in the literature were studied and compared in detail, and the conditions for the improved separation of a group of eight HAA are discussed. The effects of buffer pH and the concentration of the organic modifier (methanol and acetonitrile) on the separation and elution order of the HAA were also studied. In addition, for the first time, the running buffer was modified with α-, β-, and γ-cyclodextrin. The overall separation was improved with β-cyclodextrin, and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) gave the strongest interaction.