Exposures to silica-containing dusts are associated with a risk of developing life-threatening lung diseases. However, the mechanism of silica toxicity is poorly understood. In this work the atomic structure of the surfaces of different silica polymorphs was determined, and a relationship with in vitro silica toxicity was examined. The density of geminal and single silanol groups was quantitatively estimated for different silica polymorphs using a novel molecular modeling method. An association was found between the reported haemolytic activity and modeled densities of surface geminal (but not single) silanol groups on several silica polymorphs. These findings suggest a new view of aerosol toxicity based on the estimation of surface site densities. The results can be used in the development of new toxicological assays for respirable particulates, including nanomaterials.