Anthropogenic activities, indiscriminate and rapid industrialization, as well as pursuance of a comfortable lifestyle have led to an increase in the use of industrial chemicals, pesticides, fossil fuels, polymers, new chemical entities, engineered nanomaterials, and nanocomposites. This has increased environmental pollution leading to adverse impact on all living beings including humans. Sensitive and robust test systems are thus required for accurate hazard identification and risk assessment. The Comet assay has been used widely as a simple, rapid, and sensitive tool for assessment of DNA damage in single cells from both in vitro and in vivo models as well as in humans. The advantages of the in vivo Comet assay are its ability to detect DNA damage in both proliferating or non-proliferating cells and its sensitivity to detect genotoxicity. The recommendations from the international workshops held for the Comet assay have established guidelines, and OECD has also adopted a guideline for the in vivo Comet assay as a test for assessing DNA damage in animals. The in vitro Comet assay conducted in cultured cells can be used for screening large number of compounds and at very low concentrations. The in vitro assay has also been automated to provide a high-throughput screening method for new chemical entities, as well as in environmental samples. This chapter details the in vitro Comet assay using the 96-well plate and in vivo Comet assay in multiple organs of the mouse.