The formation of nanometer-scale silicon dots on ultrathin SiO2 layers has been studied by controlling the early stages of low-pressure chemical vapor deposition (LPCVD) of a monosilane gas. It has been suggested that the thermal dissociation of surface Si-O bonds plays a role in creation of nucleation sites on as-grown SiO2 and that surface Si-OH bonds formed by a dilute HF treatment or pure water immersion act as nucleation sites during LPCVD. By spatially controlling OH-termination on the SiO2 surface before LPCVD, the selective growth of Si dots has been demonstrated.