The potential use of affinity capillary electrophoresis in a microscale search for mutually interacting substances in biological fluid is demonstrated. Some disaccharides, especially gentiobiose (Gen), derivatized with 1-phenyl-3-methyl-5-pyrazolone, caused peak retardation when electrophoresed in a neutral running buffer, containing human serum. Gen, the most significantly retarded disaccharide, was converted to its negatively charged bis-mercaptoethanesulfonate derivative (MerESGen), and a serum sample was analyzed in a neutral buffer containing the derivatized disaccharide. Two peaks, belonging to the beta-globulin fraction, were found to be remarkably retarded in the buffer containing MerES-Gen in a concentration-dependent way. These findings prove an interaction between disaccharides and serum proteins.