The Food Safety Commission (FSC) was founded in 2003 to conduct the risk assessment of chemicals in food and food products and also residues of agricultural chemicals. Genotoxicity assessment is one component of the overall risk assessment process. Historically, genotoxicity assessment has been limited mainly to qualitative hazard identification. We are proposing a strategy for when the chemical is classified as a genotoxic carcinogen and the acceptable daily intake (ADI) cannot be set because a worldwide consensus has not been obtained on the existence of threshold for DNA direct-acting genotoxicity. To evaluate the mechanism(s) of carcinogenicity, it is important to make judgment whether genotoxicity, especially genotoxicity/mutagenicity resulting from direct reaction with DNA, is a key event or not in the carcinogenic process. Here, we focus on the residues of agricultural chemicals and discuss the strategy of how to evaluate and interpret genotoxicity, and provide guidance that we can use at the site of assessment. This paper presents the authors' personal opinion and it does not necessarily represent the official opinion of the FSC. There are four independent expert working groups in the Expert Committee for evaluation of agricultural chemicals and the authors hope this paper will help to make evaluation fair and transparent across the working groups. Of course, other strategies to evaluate genotoxicity of food and food related chemicals, including residues of agricultural chemicals may also exist, and they should also be appreciated. The goal is scientifically sound, transparent, and fair evaluation and interpretation of genotoxicity, as an integral part of the risk assessment.