The influence of diets rich in saturated fats and simple sugars on the intestinal microbiota plays a central role in obesity. Being overweight or obese predisposes individuals to several diseases including oesophageal adenocarcinoma (OAC), which develops through a cascade of events starting with gastro-oesophageal reflux disease, progressing to Barrett's oesophagus (BO), and then OAC. A range of mechanisms for the increased risk of OAC in obese individuals have been proposed; however, a role for the oesophageal microbiota has been largely ignored. This is despite the fact that it is clear that the composition of the oesophageal microbiota shifts with the development of OAC. Given the well-established impact that unhealthy diets have on the intestinal microbiota, it is plausible that exposure to unhealthy foods, and the ensuing obesity, would result in an imbalance in the oesophageal microbiota. It is also likely that these changes may mimic the changes observed in the intestinal microbiota (i.e. increase in short-chain fatty acid (SCFA) producers and bile acid biosynthesis). The modulation of SCFAs and bile acids in the oesophagus by diet could promote the transdifferentiation from squamous to intestinal-like columnar cells observed in BO, given that intestinal cells proliferate in the presence of SCFAs.