Au, Ag, Se, and Si nanoparticles were synthesized from aqueous solutions of HAuCl4, AgNO3, Na2SeO3, and Na2SiO3 with extra- and intracellular extracts from the xylotrophic basidiomycetes Pleurotus ostreatus, Lentinus edodes, Ganoderma lucidum, and Grifola frondosa. The shape, size, and aggregation properties of the nanoparticles depended both on the fungal species and on the extract type. The bioreduction of the metal-containing compounds and the formation rate of Au and Ag nanoparticles depended directly on the phenol oxidase activity of the fungal extracts used. The biofabrication of Se and Si nanoparticles did not depend on phenol oxidase activity. When we used mycelial extracts from different fungal morphological structures, we succeeded in obtaining nanoparticles of differing shapes and sizes. The cytotoxicity of the noble metal nanoparticles, which are widely used in biomedicine, was evaluated on the HeLa and Vero cell lines. The cytotoxicity of the Au nanoparticles was negligible in a broad concentration range (1–100 µg/mL), whereas the Ag nanoparticles were nontoxic only when used between 1 and 10 µg/mL.