Although silica particles have been used for tooth polishing, polishing with nanosized particles has not been reported. Here we hypothesize that such polishing may protect tooth surfaces against the damage caused by cariogenic bacteria, because the bacteria can be easily removed from such polished surfaces. This was tested on human teeth ex vivo. The roughness of the polished surfaces was measured with atomic force microscopy (AFM). A considerably lower nanometer-scale roughness was obtained when silica nanoparticles were used to polish the tooth surfaces, as compared with conventional polishing pastes. Bacterial attachment to the dental surfaces was studied for Streptococcus mutans, the most abundant cariogenic bacteria. We demonstrated that it is easier to remove bacteria from areas polished with silica nanoparticles. The results demonstrate the advantage of using silica nanoparticles as abrasives for tooth polishing.