Diet is well known to have beneficial health properties that extend beyond traditionally accepted nutritional effects. The approach involved in elucidating these beneficial physiological effects is becoming more important, as reflected by increasing research being undertaken. With growing consumer awareness of foods and food constituents and their relationship to health, the key questions for regulators, scientists and the food industry continue to relate to: (1) how consumers could be protected and have confidence that the health claims on foods are well supported by the evidence; (2) how research on physiological effects of food (constituents) and their health benefits could be stimulated and supported; (3) how research findings could be used in the development of innovative new food products. The objectives of this paper are to provide a set of recommendations on the substantiation of health claims for foods, to develop further guidance on the choice of validated markers (or marker patterns) and what effects are considered to be beneficial to the health of the general public (or specific target groups). Finally, the case for developing a standardised approach for assessing the totality of the available scientific data and weighing the evidence is proposed.