This Opinion discusses the risk assessment issues associated with Genetically Modified (GM) plants used for non-food or non-feed purposes (e.g. for the production of industrial or medicinal products, biofuel or for phytoremediation), and outlines the applicable legal framework and the recommended scientific methods for their risk assessment. A comparative approach is advocated but will need to be applied carefully. Consumption is not expected with these GM plants used for non-food or non-feed purposes, but accidental oral, dermal, ocular and inhalatory exposure is possible and assessments of toxicity and allergenicity are discussed. This Opinion recommends that exposure assessments take account of any strategies to reduce exposure or gene flow proposed by the applicant. It is considered that existing guidance on the environmental risk assessment of GM plants is adequate but that additional emphasis should be given to issues such as gene transfer and the exposure of non-target organisms, particularly wildlife feeding on these GM plants. The Opinion further describes the importance of risk management systems, such as post-market environmental monitoring, standard production protocols/stewardship, or confinement strategies to reduce exposure to the GM plant.