Amorphous silicas, opposite to crystalline polymorphs, have been regarded so far as nonpathogenic, but few studies have addressed the toxicity of the wide array of amorphous silica forms. With the advent of nanotoxicology, there has been a rising concern about the safety of silica nanoparticles to be used in nanomedicine. Here, we report a study on the toxicity of amorphous nanostructured silicas obtained with two different preparation procedures (pyrolysis vs. precipitation), the pyrogenic in two very different particle sizes, in order to assess the role of size and origin on surface properties and on the cell damage, oxidative stress, and inflammatory response elicited in murine alveolar macrophages. A quartz dust was employed as positive control and monodispersed silica spheres as negative control. Pyrogenic silicas were remarkably more active than the precipitated one as to cytotoxicity, reactive oxygen species production, lipid peroxidation, nitric oxide synthesis, and production of tumor necrosis factor-α, when compared both per mass and per unit surface. Between the two pyrogenic silicas, the larger one was the more active. Silanols density is the major difference in surface composition among the three silicas, being much larger than the precipitated one as indicated by joint calorimetric and infrared spectroscopy analysis. We assume here that full hydroxylation of a silica surface, with consequent stable coverage by water molecules, reduces/inhibits toxic behavior. The preparation route appears thus determinant in yielding potentially toxic materials, although the smallest size does not always correspond to an increased toxicity.