poly-dimethylsiloxane (PDMS) microchip. Homocysteine is a major causative agent that can result in vascular disease. It is reported that the higher the concentration of homocysteine in the blood, the higher the incidence of vascular disease. Thus, accurate separation and analysis of homocysteine are crucial. This experiment is aimed at analyzing the homocysteine by using capillary electrophoresis on a microchip in a more easily and quickly manner than the conventional method. However, the PDMS microchip, which is currently a major chip, has the advantage that the chip can be easily fabricated in a laboratory while showing the disadvantage that the chemical structure of the channel inner wall becomes unstable over time. Thus, to overcome this disadvantage, the channel inner wall was chemically and physically modified by using cethyltrimethylammonium bromide (CTAB), which is a cationic surfactant, as well as polyethylene oxide (PEO), which is a linear polymer, which resulted in stabilized fluid flow. The capillary electrophoresis analysis experiment on the modified microchip showed that the separation and analysis of homocysteine and thiol-containing amino acids were achieved in a short time (within 90 seconds) with significantly high separation efficiency. Furthermore, the results have confirmed that the chip using CTAB has a separation efficiency of approximately 17 to 20 times higher than that of the chip using PEO. This study could be applicable as a biosensor in the disease diagnostics field in the future.