The European Food Safety Authority mandated its GMO Unit to prepare a statement supporting the application of the EFSA Scientific Committee ‘Guidance on conducting repeated‐dose 90‐day oral toxicity study in rodents on whole food/feed’ in the frame of Implementing Regulation (EU) 503/2013, which requires a 90‐day study in rodents for the risk assessment of genetically modified (GM) plants. This statement illustrates two possible scenarios for 90‐day studies, based on the identification (scenario 1) or not (scenario 2) of hazards in previous analyses, and provides information on the study design, conduct and interpretation accordingly. Considerations on the type and source of the test materials and on preparation of test diets are also provided, with illustrative examples. Detailed analytical characterisation of the test and control materials and diets are recommended, including the detection of the genetic event and, if appropriate, quantification of the newly expressed protein(s). The selection of dose levels is discussed, with a maximum incorporation rate (high dose level) proposed for various crops. The selection of one dose level only (the high dose) is proposed as an option and discussed for scenario 2. The preferred test species is the rat; it should be socially housed, single housing needing justification. Limitations for the identification of appropriate sample sizes are discussed for both scenarios. Technical details for endpoints selection and data collection are provided. Strategies for integrated study interpretation are presented and areas for further scientific development are discussed.