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The key factor and mechanism for reported toxicity of CNTs are unclear. Here we firstly quantify the contribution of metal residues and fiber structure to the toxicity of CNTs. Significant quantities of metal can be mobilized from CNTs into surrounding fluids, depending on the properties and constituent of biological microenvironment and metal particles. Hydroxyl radicals were generated by CNT containing metal impurities and leachable metal, while several inherent biomolecules facilitate the generation of free radical. Cell viability is highly dependent on the amount of metal residues and iron in particular but not tube structure, while the negative effect of CNT was limited in a certain concentration range below 80 μg ml−1.