In this work the electrophoretic behaviour of hydrophobic fullerenes (C60, C70 and C60-pyrr) and water soluble fullerenes (C60(OH)24, C120(OH)30, C60-pyrr tris acid and C60CHCOOH) in micellar electrokinetic capillary chromatography (MECC) was evaluated. The aggregation behavior of the water soluble compounds in MECC at different buffer and SDS concentrations and pH values of the background electrolyte (BGE) was studied by monitoring the changes observed in the electrophoretic pattern of the peaks. Broad and distorted peaks that can be attributed to fullerene aggregation were obtained in MECC which became narrower and more symmetric by working at low buffer and SDS concentrations (below the critical micelle concentration, capillary zone electrophoresis (CZE) conditions). For the characterization of the suspected aggregates formed (size and shape), asymmetrical flow field-flow fractionation (AF4) and transmission electron microscopy (TEM) were used. The results showed that the increase in the buffer concentration promoted the aggregation of the particles while the presence of SDS micelles revealed multiple peaks corresponding to particles of different aggregation degree. Furthermore, MECC has been applied for the first time for the analysis of C60 in two different cosmetic products (i.e., anti-aging serum and facial mask).