The orientation of pterin-6-carboxylic acid on gold nanopillars was investigated by surface enhanced Raman spectroscopy and density functional theory methods.The experimentally vibrations from pterin-6-COOH free and attached to the Au surface display vibration features indicating chemical interaction of the pterin with the metal surface.The spectral feature evidenced that the pterin would adsorb on gold surface with a "lying down" configuration through the high intensity vibration of NH scissoring and rocking OH modes.The orientation study of pterins on gold nanopillars presented herein is believed to lead to new applications in biosensing field for detecting pterins of physiological importance.