We have studied the chemisorption of benzene and pyrazine on Si(001)-2×1 at room temperature using photoelectron diffraction (PED). For benzene, comparison between the experimental and simulated PED patterns with R-factor analysis leads to the conclusion that a di-σ-bonded configuration is mainly formed at the saturation coverage. For pyrazine, the PED results show that the double dimer bridging configuration is formed, in which pyrazine molecule forms a bridging between the dimer rows with the two Si-N bonds.