The main goal of this research was to study the interactions of a fully characterized set of silver nanomaterials (Ag ENMs) with cells in vitro, according to the standards of Good Laboratory Practices (GLP), to assure the quality of nanotoxicology research. We were interested in whether Ag ENMs synthesized by the same method, with the same size distribution, shape and specific surface area, but with different charges and surface compositions could give different biological responses. A range of methods and toxicity endpoints were applied to study the impacts of interaction of the Ag ENMs with TK6 cells. As tests of viability, relative growth activity and trypan blue exclusion were applied. Genotoxicity was evaluated by the alkaline comet assay for detection of strand breaks and oxidized purines. The mutagenic potential of Ag ENMs was investigated with the in vitro HPRT gene mutation test on V79-4 cells according to the OECD protocol. Ag ENM agglomeration, dissolution as well as uptake and distribution within the cells were investigated as crucial aspects of Ag ENM toxicity. Ag ENM stabilizers were included in addition to positive and negative controls. Different cytotoxic effects were observed including membrane damage, cell cycle arrest and cell death. Ag ENMs also induced various kinds of DNA damage including strand breaks and DNA oxidation, and caused gene mutation. We found that positive Ag ENMs had greater impact on cyto- and genotoxicity than did Ag ENMs with neutral or negative charge, assumed to be related to their greater uptake into cells and to their presence in the nucleus and mitochondria, implying that Ag ENMs might induce toxicity by both direct and indirect mechanisms. We showed that Ag ENMs could be cytotoxic, genotoxic and mutagenic. Our experiments with the HPRT gene mutation assay demonstrated that surface chemical composition plays a significant role in Ag ENM toxicity.