Cyclic olefin copolymer (COC) based microfluidic devices offer unique opportunities in developing high quality chips for a variety of applications but critical issues such as the bonding strength, biocompatibility and flow need to be addressed before this can be realized. In this study, we introduce a simple microfluidic device fabricated on COC (Topas) substrates that were modified by ultraviolet (UV) photo-grafting of a hydrophilic monomer 2-hydroxyethyl methacrylate (HEMA). This water soluble acrylic monomer was used to increase the bond strength, surface wettability and hemocompatibility. Thermal bonding of the microfluidic chips was accomplished at temperatures well below the glass transition temperature (T_g) of the COC polymer. Moreover, this process produced COC microchannels with modified surfaces that had stable permanent hydrophilic properties. Therefore, it can be used for Bio-MEMS applications in electrophoretic analysis where stable electro-osmotic flow (EOF) is important. The bond strength and burst pressure of the HEMA modified chips increased significantly to 1.70 MPa and 4.20 MPa for bonding at 10 °C below T_g. The COC surfaces were characterized using contact angle, EOF measurements, and Fourier transform infrared spectroscopy. The hydrophilicities of the substrates improved significantly with increase in degree of poly-HEMA immobilization and a maximum grafting yield of about 0.13% was obtained for a short irradiation time of 12 min with 25% of HEMA monomer. In vitrofibrinogen and fluorescent labeled bovine serum albumin adsorption results indicated that the COC surface can easily be tuned against protein adsorption by controlling the grafting yield. The in vitroplatelet adhesion tests confirmed that the hydroxyl functionality greatly improved the surface hemocompatibility of COC by reducing the number and the degree of activation of the adherent platelets.