Coeliac disease (CD) is a disorder resulting from interactions between diet, genome and immunity. This research seeks to further our understanding of the pathology of CD in regard to its secondary effects on the diversity of enteral microflora via changes in immune tolerance. It proposes that enteral mucosal pro-inflammatory change in CD is associated with a decrease in microbial diversity whilst remission from inflammation may result in an increase in enteral microbial diversity that could contribute to the restoration of tolerance. The first study analyses whether remission from active CD is associated with change in generic enteral microbial diversity by assessing people at diagnosis and following their response to gluten exclusion. A comparison is made to people without CD consuming a ’normal diet’. DGGE profiling of faecal microflora in subjects with CD at diagnosis (confirmed by serology and by duodenal biopsy) and over three consecutive months on a gluten-free diet (GFD) was performed and profiles were compared with those of age and gender matched control subjects taken at monthly intervals. Diversity of faecal microflora (measured as Simpsons Index ) was significantly lower in people with CD than in control subjects. It was possible to distinguish the profiles of coeliac subjects at diagnosis from those obtained after three months on a GFD but it was not possible to distinguish between the samples from control subjects taken at monthly intervals. The profiles of CD subjects after three months on a GFD were more dissimilar to those of the control subjects than those obtained prior to dietary treatment, chiefly on the basis of three bands that were not found in the faeces of any control subjects. The second study analyses dietary intake to determine if a lack of nutrients at diagnosis (before institution of a GFD) and at monthly intervals for three consecutive months post diagnosis (on a GFD) exists, as it is known that CD is associated with nutrient deficiencies resulting from malabsorption due to intestinal inflammation and damage. Subjects completed a customised food questionnaire at each sampling period. Dietary intake was analysed using Foodworks Professional 2007. Significant differences were identified in gluten, starch and carbohydrate intake but not in other macronutrients. Contrary to established literature, these analyses identified few significant differences in micronutrient intake within coeliac subjects over time, however, significant differences were found in iron and sodium.