Chemical and physical effects of plasma exposed Si wafer pairs were investigated on Si wafer bonding. Oxygen plasma treated Si wafer pairs bonded more strongly at room temperature compared to chemically cleaned, hydrophilic and hydrophobic Si. After 50 hours of annealing at 105°C, the surface energy of the bonded Si pair reached the surface energy of bulk Si (100). X- ray photoemission spectroscopy (XPS) measurements indicated that the exposure of both hydrophilic and hydrophobic Si to oxygen plasma increased a SiO2 like state in the surface layer to a depth of 1.5 nm. Atomic force microscopy (AFM) study showed that plasma irradiation at 300 watts up to 30 seconds did not change surface roughness below 0.5 nm. Exposure to He plasma or N2 did result in enhanced bonding after annealing at 165°C, however, over smaller areas.