In public debate GMPs are often referred to as being unnatural or a violation of nature. Some people have serious moral concerns about departures from what is natural. Others are concerned about potential risks to the environment arising from the combination of hereditary material moving across natural boundaries and the limits of scientific foresight of long-term consequences. To address some of these concerns we propose that an additional element in risk assessment based on the concept of familiarity should be introduced. The objective is to facilitate transparency about uncertainties inherent in the risk assessment of the GMP. Familiarity conventionally involves data and experience relating to the plant species and the ecosystem in question. We would like to extend this concept to the molecular level of plant breeding and suggest that GMP characteristics should be compared to a reference baseline determined by conventional breeding techniques. Three GMPs are ranked according to familiarity at the plant and ecosystem level and the molecular level. The approach may help to integrate discussion of the scientific arguments and moral questions raised in the debate about GMOs by providing an operational scheme within which moral concerns are brought within the framework of science-based risk assessment.