This review discusses the utility and limitations of model gut systems in accurately modelling the mucosa of the digestive tract from both an anatomical and functional perspective, with a particular focus on the oesophagus and the upper digestive tract, and what this means for effective in vitro modelling of oesophageal pathology. Disorders of the oesophagus include heartburn, dysphagia, eosinophilic oesophagitis, achalasia, oesophageal spasm and gastroesophageal reflux disease. 3D in vitro models of the oesophagus, such as organotypic 3D culture and spheroid culture, have been shown to be effective tools for investigating oesophageal pathology. However, these models are not integrated with modelling of the upper digestive tract—presenting an opportunity for future development. Reflux of upper gastrointestinal contents is a major contributor to oesophageal pathologies like gastroesophageal reflux disease and Barratt’s oesophagus, and in vitro models are essential for understanding their mechanisms and developing solutions. The limitations of current model gut systems in modelling the mucosa is not only limited to the oesophagus. Integration of modelling of the mucus covered epithelia of the stomach and small intestine in to upper digestive tract models is limited and often not considered at all. In this paper we discuss mucus structure and function and current approaches to modelling of the mucus layer in isolation, and in integrated systems with cell culture systems and digestive models. We identify a need for relevant modelling of the viscoelastic properties of mucus and its protective function to allow complete integration in modelling. Addressing limitations of current in vitro models and integrating upper gastrointestinal models with those of the oesophagus presents an opportunity for better understanding oesophageal physiology and pathophysiology where reflux of digestive fluids is involved.