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Exclusive enteral nutrition (EEN) is a prescribed liquid diet providing 100% of energy intake while excluding all other foods and drinks. It uses polymeric or elemental formulas, which are equally effective, though polymeric formulas are more palatable and better tolerated over 6–8 weeks. EEN is established as an effective therapy for Crohn's Disease (CD) that induces remission in up to 80% of patients [1, 2]. The clinical benefits of EEN include (a) the reduction of inflammation, with decreases in both blood and gut inflammatory markers and induction of mucosal healing, and (b) the improvement of clinical and physical health, with promotion of clinical remission and enhancement of muscle mass and nutritional status [3]. Studies have shown that EEN induces significant changes in the microbiome; although these changes are implicated in each mechanism of action, further research is needed to provide a better understanding of diet–microbiome interactions in CD [4, 5]. In the present article, the Bradford Hill criteria [6], a set of principles used to determine causal relationships between an exposure and a disease, are employed as a framework to analyse the EEN–microbiome interactions in CD. These criteria include factors such as strength, consistency, temporality and biological plausibility [6].