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# The Author(s) 2015. This article is published with open access at Springerlink.com Abstract We discuss eight major challenges in the field of carbon nanomaterial toxic-ity. Generally, we pick up some of them, and the most important challenge is searching of the qualitative relationships between nanofactors and cytotoxicity. This is important since it can provide the possibility of conscious changes of carbon nanotubes cytotox-icity by manipulation with selected nanofactors. Therefore, the toxicity of a series of gradually oxidized carbon nanotubes is studied. We show, for the first time, that toxicity of those materials depends strongly on the ratio of acidic to basic group concentration—the higher is this ratio value, the more toxic are nanotubes. In this way, by changing this ratio, one can change toxicity. This correlation is more evident after ultrasonication, and it is connected with the accessibility of charged groups for interactions with proteins. Toxicity also depends on the ability of nanotubes for protein adsorption. We suggest that the changes in the protein composition of medium, especially lack of important growth factors, inhibit cell proliferation