Coeliac disease is defined as a permanent gluten sensitive enteropathy. The classical mucosal lesion is of villous atrophy, crypt hypertrophy and lymphocyte infiltration of the epithelium. It is now generally agreed that a spectrum of mucosal damage exits ranging from total villous atrophy to normal villous architecture with increased numbers of intraepithelial lymphocytes (IEL). Gluten sensitivity can still be demonstrated in this minimal lesion, with the IEL count falling with withdrawal of gluten and rising again on gluten challenge. In the first part of this thesis I will present work validating computerised image analysis as a method for quantifying IEL in small bowel biopsy in order to identify individuals with minimal change given gluten sensitive pathology. Antibodies to the gliadin fraction of gluten and also to an as yet unidentified tissue antigen occur in coeliac disease. These antibodies are useful in the initial diagnosis of coeliac disease as well as in monitoring response to treatment and timing of biopsy following oral gluten challenge. They are also used in the screening of individuals who have a higher incidence of coeliac disease. In the next section of my thesis I will describe the development of a newly described assay for antiendomysium antibody both for research and also for the routine NHS clinical service in Lothian. Progress in the application of strict criteria for the diagnosis of gluten sensitivity has been hampered by the fact that currently the only evidence is based on clinical and pathological effects of gluten withdrawal and challenge which may take several months or years and requires multiple invasive small bowel biopsies. For this reason rectal challenge with gluten is being considered as a possible alliterative method for demonstrating gluten sensitivity. Currently this requires computerised image analysis of multiple rectal biopsies.