A novel polydimethylsiloxane (PDMS) surface modification method for microchip electrophoresis has been developed to make a stable and sufficient electroosmotic flow (EOF). Poly(l-glutamic acid) (PGA) which had ionizable carboxyl groups at a high pH-range was immobilized on the surface of microchannel fabricated with PDMS. The surface modification involved surface oxidation by plasma, the silanization of 3-aminopropyldimethylethoxysilane (APDMES) and immobilization of PGA via amide bond. The modified channel was extremely stable against consecutive electric power supply over 5h, and its long-term stability was demonstrated by the efficient separation of four amino acid derivatives reproducibly after a week. Additionally, homocysteine (Hcy), important risk factor of cardiovascular disease, osteoporosis and problems in pregnancy, was successfully measured in human serum in modified PDMS channel with the other thio amino acid simultaneously.