The behavior of two different fractions of the electrically conducting polymer polyaniline (PANI) was studied in order to characterize them using fast, simple, and cheap methods of capillary zone electrophoresis. In contradistinction to the expectations that the particles will bear a positive charge on their surface, in the milieu of electrolytes used for electrophoresis (0.01-0.05 M buffers of pH 4-8.5), the surface was demonstrated to be slightly negatively charged, which led to a slow migration to the anode. An evident charge was given to the particles after their interaction with micelles formed from surface active components, cetyltrimethylammonium bromide (CTAB) and sodium dodecyl sulfate (SDS). An active electrophoretic migration and full separation of the PANI fractions was achieved by micellar electrokinetic chromatography (MEKC) with negatively charged SDS micelles. With this method, a reliable qualitative as well as quantitative analysis was performed in the concentration range of 0.1-1.6 mg/mL with a reproducibility of migration times better than 1.5%.