Although silicon (Si) nanostructures exhibit size dependent light emission, which can be attributed to quantum confinement, the role of surface passivation is not fully understood. Si nanocrystals less than 6 nm in diameter are grown on SiO2 surfaces in an ultrahigh vacuum chamber using hot wire chemical vapor deposition. The surface chemistry of deuterium-passivated Si nanocrystals is studied using temperature programed desorption to follow the formation of surface deuterides and amorphization of Si nanocrystals. The influence of the surface deuteride species and amorphization on the photoluminescence (PL) emitted from Si nanocrystals is reported for an excitation wavelength of 405 nm. No PL is observed from the as-grown unpassivated nanocrystals. The as-grown surfaces are exposed to atomic deuterium at 375 K and PL is measured at 310–315 K. As the deuterium dose is increased, the PL intensity also begins to increase. This can be associated with increasing amounts of mono-, di-, and trideuteride species on the nanocrystal surface, which results in better passivation of the dangling bonds. At high deuterium doses, the surface structure breaks down and amorphization of the top layer of the nanocrystal takes place. Amorphization reduces the PL intensity. Finally, as the nanocrystal size is varied, the PL peak shifts, which is characteristic of quantum confinement.