The Nuclear Energy Agency organised its third workshop on ‘Science and values in radiological protection’ in November 2012 in Tokyo. One of the issues addressed, non-cancer effects, had also been addressed in the first two science and values workshops (Helsinki, Finland, 2008; Vaux-de-Cernay, France, 2009), but presented several new elements of relevance to International Commission on Radiological Protection discussions of the evolution of the system of radiological protection. Radiological protection science, both epidemiological and biological, now suggests that stroke and heart disease may well be caused by radiation exposure at doses of the order of 0.5 Gy or less. Further, it is possible that such detriments may be caused by either chronic or acute exposures. While significant uncertainties remain, the need to consider non-cancer detriment in risk assessment and in the development of protection strategies is now a significant scientific and ethical question. This paper will present the results of the Nuclear Energy Agency science and values workshop discussion of non-cancer risks, and of the questions and possible future directions raised during the workshop.