Silver nanocrystals encapsulated in mesoporous silica nanoparticles are prepared by coating hydrophobic silver nanocrystals with amphiphilic surfactants and growing mesostructured silica around the materials. The nanoparticles can be used as antimicrobial agents for both Gram-positive and -negative bacteria through oxidative dissolution of the silver nanocrystals. The surface characteristics of the silica exterior affect the binding to the bacteria and the cytotoxicity.