Concomitant with the increase in production and application of various nanomaterials, researches on their cytotoxic and genotoxic potential have become well established, as exposure to these nanoscaled materials may contribute to detrimental health effects. Positive indications of the damaging effects of nanoparticles on DNA are likely to be inconsistent in in vitro systems, and thus the implementation of in vivo investigations has been achieved. This review summarizes the current results, both in vitro and in vivo, of the genotoxic effects of potential metal or metal oxide nanoparticles, including the oxides of aluminium, iron, silica, titanium, and zinc, as well as silver, gold, cobalt, quantum dots, and so forth. They present indications of different types of DNA damage, ranging from chromosomal aberrations, through DNA strand breaks, oxidative DNA damage, to mutations. Their toxicological profiles are definitely associated with physicochemical characters, depending upon the characterization methods by which they are analyzed, in particular, microscopy techniques. Besides physicochemical properties, we also discuss significant parameters that may influence genotoxic response, including toxicity assays/endpoint tests, exposure duration and route of exposure, and experimental conditions. We describe advantages and disadvantages of particular characterization methods, as well as the appropriateness of methodologies for investigating physicochemical characters. Therefore, recommendations on particle characterization are further emphasized, to provide better understanding of genotoxic potential.