Protein protein conjugates formed by carbodiimide crosslinking reactions have been analyzed for the first time using CE Lysozyme and BSA were chosen as model proteins to study the efficacy of N-(3-dimethylaminopropyl)-N-ethylcarbodiimide and N-hydroxysuccinimide as closslinkers Detection of the molecular mass increase was checked by SDS-PAGE Commercially available, PVA-coated capillaries showed appropriate selection, while phospho-deactivated and dynamic PVA-coated capillaries did not give suitable resolution. CE was found to be an efficient tool to characterize homo- (lysozyme lysozyme) and hetero-(lysozyme BSA) protein coupling by suitable variations of electrophoretic mobilities.