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In the last two decades the production and use of nanomaterials (NMs) has impressively increased. Their small size, given a mass equal to that of the corresponding bulk material, implies an increase in the surface area and consequently in the number of atoms that can be reactive. They possess different physical, chemical and biological properties compared to bulk materials of the same composition, which makes them very interesting and valuable for many different applications in technology, energy, construction, electronics, agriculture, optics, paints, textiles, food, cosmetics, medicine... Toxicological assessment of NMs is crucial; the same properties that make them interesting also make them potentially harmful for health and the environment. However, the term NM covers many different kinds of particle , and so there is no simple, standard approach to assessing their toxicity. NMs can enter the cell, interact with cell components and even penetrate the nucleus and interfere with the genetic material. Among the different branches of toxicology, genotoxicity is a main area of concern since it is closely related with the carcinogenic potential of compounds. The Organisation for Economic Co-operation and Development (OECD) has published internationally agreed in vitro and in vivo validated test methods to evaluate different genotoxic endpoints of chemicals, including chromosome and gene mutations, and DNA breaks. However not all the assays are suitable to study the genotoxic potential of NMs as has been shown by the OECD Working Party on Manufactured Nanomaterials (WPMN). Moreover, alterations to DNA bases, which are precursors to mutations and of great importance in elucidating the mechanism of action of NMs, are not covered by the OECD guidelines. The in vivo standard comet assay (which measures DNA breaks and alkali-labile sites) was included in the OECD assays battery in September 2014 while the in vitro standard comet assay is currently under validation. The comet assay has not been yet proposed as an appropriate test to check the genotoxic potential of NMs, though at a research level it is the most used in vitro assay and the second most used in vivo assay. Moreover, the combination of the comet assay with enzymes that convert altered bases to breaks allows the identification of DNA damage induced by secondary mechanisms (e.g. oxidative stress induced by inflammation), which is very relevant in the case of NMs. Possible problems with the use of the comet assay have been suggested: NMs have been detected in close association with comets, and might interact with the DNA; or NMs might inhibit the action of enzymes. However, control experiments have not confirmed that these interactions are significant.