Allium cepa (A. cepa) root tip assay is considered an excellent genetic model for genotoxicity screening and monitoring of environmental mutagens. The assay is highly versatile for genetic endpoints, inexpensive, quick, and easy to use. It can be used with a range of environmental conditions, pH, and temperature, and does not require any ethical regulations as required for animal models and cell lines. In this chapter, we describe the modifications of the assay to analyze different endpoints of genotoxicity. They include the most commonly used chromosome aberrations, the mitotic index to evaluate cytotoxicity, and the analysis of micronuclei to verify the mutagenicity of different chemicals. Moreover, the A. cepa test system also provides a sensitive method for the evaluation of DNA damage and DNA repair capacity at the single-cell level by the Comet assay.