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The literature pertaining to non-IgE immune-mediated adverse reactions to foods has been reviewed and ranked with regards to the quality of evidence that the conditions are (1) triggered by foods and (2) have an immunological mechanism which is distinct from IgE-mediated food allergies. The condition that met both criteria is the gluten intolerance syndrome, comprising Coeliac disease (CD), and the associated conditions dermatitis hepertiformis (DH) and gluten ataxia (GA). Food protein induced enterocolitis syndrome partly met the criteria. Whilst food has been implicated as the trigger for other conditions its role in the disease process is not clearly defined. These include food protein induced enteropathies frequently experienced early in life, Heiner Syndrome and eosinophilic gut disease, such as eosinophilic oesophagitis. Conditions like Heiner Syndrome are very rare. The literature regarding non-IgE mediated reactions being triggered by feed in farm and companion animals is limited. CD, DH and GA were also the conditions with the clearest clinical diagnostic criteria for which in vitro diagnostic tools had been validated. Data on the prevalence of CD were also considered to be of the highest quality. The sequences of coeliac-toxic motifs in gluten have been defined, and play a clear role in the pathogenesis of CD, DH and GA. Thus, it is possible to assess whether a newly expressed protein contains coeliac-toxic motifs which have the potential to trigger CD and its associated conditions. The methodology used for characterising CD could be readily adapted and incorporated into the current allergenicity risk assessment process, including, for example, in silico analysis, resistance to digestion and an assessment of the capacity of novel coeliac toxic motifs to activate T-cells.