The toxicological effects of nanoparticles (NPs) on humans, animals, and environment are largely unknown. Assessment of NPs cytotoxicity depends on the choice of the test system. Due to NPs optical activity and absorption values, they can influence the classical cytotoxicity assay. Eight NPs were spiked in the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and crystal violet assays and tested with HaCaT human skin cells. The MTT assay standard curve optical density (OD) measurements were altered by the presence of trisilanol phenyl and trisilanol isooctyl polyhedral oligomeric silsesquioxane particles. The crystal violet standard curve OD measurements were significantly shifted by gold NPs, but they did not affect the MTT assay. Carbon black decreased ODs in the MTT and crystal violet assays and was localized in the cell cytoplasm. These findings strongly indicate that a careful choice of in vitro viability systems is required to avoid flawed measurement of NPs toxicity.