Plastic microchips are very promising analytical devices for the high-speed analysis of biological compounds. However, due to its hydrophobicity, their surface strongly interacts with nonpolar analytes or species containing hydrophobic domains, resulting in a significant uncontrolled adsorption on the channel walls. This paper describes the migration of fluorescence-labeled amino acids and proteins using the poly(methyl methacrylate) microchip. A cationic starch derivative significantly decreases the adsorption of analytes on the channel walls. The migration time of the analytes was related to their molecular weight and net charge or p/ of the analytes. FITC-BSA migrated within 2 min, and the theoretical plate number of the peak reached 480 000 plates/m. Furthermore, proteins with a wide range of p/ values and molecular weights migrated within 1 min using the microchip.