Coeliac disease and other disorders of the small intestine are associated with disturbances in mucosal architecture. The most severe injury to tissue architecture is villus atrophy. In coeliac disease, molecules reflecting the state of the villus architecture are not well characterized at present. Expression of acyl-CoA-synthetase 5 (ACS5) was studied in unaffected human small/large intestinal tissue and in coeliac disease using several methods including molecular techniques, as well as an in situ approach using a novel established monoclonal antibody directed against human ACS5. Strong expression, synthesis, and enzymatic activity of ACS5 were found in normal small intestinal mucosa compared with unaffected colon mucosa. In normal small intestine, ACS5 preferentially located to the epithelium covering villi. In coeliac disease, expression of ACS5 was regularly associated with differentiation of villi. Thus, ACS5 was found in the villus epithelium of the small intestine with coeliac disease of Marsh grades I, II, IIIa, or IIIb respectively. In Marsh grade IIIc coeliac disease lesions, strong expression of ACS5 was detectable neither in the surface epithelium nor in the epithelium lining hyperplastic crypts. These data suggest that ACS5 is a very suitable marker molecule for the detection of villus atrophy in the small intestine.