The structure and chemistry of interfaces of directly bonded Si/Si wafer pairs after annealing at 1100°C were investigated by secondary ion mass spectroscopy (SIMS), multiple internal reflection spectroscopy (MIRS), and high resolution electron microscopy (HRTEM). Si-O, SiO-H, and Si-Hx bonds are shown to be the main atomic bonds at the interfaces of bonded hydrophilic wafer pairs, whereas Si-Si and Si-Hx bonds are dominant at interfaces of bonded hydrophobic wafer pairs. For bonded hydrophobic wafer pairs a frequency shift of the Si-Hx modes suggest that fluorine is probably present in Si-F· · ·H-Si configurations. Strongly oriented SiO-H modes detected in bonded hydrophobic wafer pairs appear to be related to oxide islands at the interface.