This paper uses the measure of hemolysis to evaluate the toxicity of nonporous and porous silica nanoparticles with varied sizes and investigates the effects of porous structure and integrity on the nanoparticle−cell interaction. The results show that both nonporous and porous silica cause red blood cell membrane damage in a concentration- and size-dependent manner. In the case of mesoporous silica nanoparticles, the size-dependent hemolysis effect is only present when the nanoparticles have long-range ordered porous structure, revealing that pore structure is critical in cell−nanoparticle interactions. Mesoporous silica nanoparticles show lower hemolytic activity than their nonporous counterparts of similar size, likely due to fewer silanol groups on the cell-contactable surface of the porous silica nanoparticles. The extent of hemolysis by mesoporous silica nanoparticles increases as the pore structure is compromised by mild aging in phosphate-buffered solutions, initiating mesopore collapse. The pore integrity of mesoporous silica nanoparticles is examined by TEM, XRD, N2 adsorption−desorption isotherms, and quantification of dissolved silica. In these nanoparticles, pore stability is clearly an important factor in determining the hemolytic activity; further work demonstrates that nanoparticle-induced hemolysis can be eliminated by modifying the silanol surface with a poly(ethylene glycol) coating.