In Europe, for authorisation of a health claim, applicants must follow the procedures in the legislation and in the guidelines for submission of a dossier set out by the European Food Safety Authority. The Functional Foods in Europe (FUFOSE) and Process for the Assessment of Scientific Support for Claims on Foods (PASSCLAIM) projects underpinned the laws and provided criteria against which the quality of the totality of the available data could be judged. Whereas the regulations and PASSCLAIM require an assessment of the extent to which cause and effect can be demonstrated between a food category, a food or constituent and a health benefit, the European Food Safety Authority requires conclusive evidence of cause and effect. This latter standard of proof and a focus on randomised controlled trials done on isolated components and using validated physiological biomarkers may not always be appropriate to assess nutrition science. The aims of this paper are to address the strengths and weaknesses of different sources of evidence that contribute to the totality of the available data, to undertake a critical examination of the application of a drug-like assessment model in evidence-based nutrition and to encourage research on new biomarkers of health and homeostatic adaptability. There is a need for (a) a robust and pragmatic scientific framework for assessing the strength, consistency and biological plausibility of the evidence, and (b) consumer understanding research on claims that use qualifying language and/or graphics to reflect the weight of evidence. Such scientific, policy and communication approaches are proportionate and could help stimulate academic research, promote fair trade and product innovation and contribute to consumer education about food and health.