Fluorinated compounds exhibit hydrophobic, nonstick, and self-cleaning properties, making them attractive for use as the coating material for biochips. In this study, we copolymerized the fluorinated compound 1H,1H,2H-perfluoro-1-decene (FD) with acrylic acid (AA) and bonded the resulting copolymer with protein G on the surface of polyelectrolyte coated polydimethylsiloxane (PDMS) to form a functional surface that captures antibodies. We demonstrated that the modified PDMS surface remained hydrophobic while becoming resistant to nonspecific protein binding. Thus, aqueous sample solutions formed the droplets (4 μL) on the surface without spreading and drying during the sample printing. Contact angle measurements showed that this functionalized surface was as hydrophobic as the native PDMS with a virtually constant contact angle over seven days of the study under dried condition at 4 °C. Spectroscopic measurements revealed that FD/AA copolymerization formed a homogeneous and highly dense multilayer (50 mg/mm(2)) with a fluorine coverage of 35.4%. Moreover, protein G was shown to covalently bind to AA molecules on the surface at a binding density of 0.24 μg/mm(2). We demonstrated that the fluorinated coating withstood nonspecific binding with extremely low background emission, leading to bioassays that, without the need of blocking agents, exhibited six times more sensitivity than PEG coatings. The fluorinated PDMS antibody microarrays were further applied to accurately determine the absolute concentration of ERα in MCF-7 cells. In conclusion, the unique properties of fluorinated compounds, such as withstanding wetting, nonspecific binding and contamination, make them an excellent coating material for use in sensitive and simple on-chip assays.