Silver nanoparticles (SNPs) were synthesized by reduction of silver ions to elementary silver in the system of β -cyclodextrin clathrates. SNPs were characterized by optical spectroscopy, microscopy (AFM, TEM), and X-ray diffractometry. Toxicity of the SNPs was tested in viruses, bacteria, yeast, cultured human cell lines, mollusks, and mammals. The particles displayed high antimicrobial activity and low toxicity in eukaryotic cells. The invertebrates were found to be more sensitive to SNPs, than mammals. Silver from SNPs was transported (apparently as Ag(I)) into the cells of prokaryotes and eukaryotes, bound to Cu(I) transport proteins. Silver was unevenly distributed between cell organelles; it was inserted to active centers of cuproenzymes and impaired their activity. The prospects to use these SNPs as antimicrobial agents, which enhance the action of antibiotics, as inhibitors of copper transport to growing tumors, and as a tool for studying copper metabolism are discussed.