The anti-transglutaminase IgA deposits in the intestinal mucosa, detected by a double-sided direct immunofluorescence (IFD) technique, are the best diagnostic marker for coeliac disease. However, this test is time consuming and largely operator-dependent. This study compared the sensibility and specificity of IgA deposits IFD-test with a new simpler test (EMA-biopsy test), based on the search of the EMA and anti-tTG antibodies in the supernatant of an intestinal mucosa fragment. One hundred thirty-four patients undergoing intestinal biopsy for suspected coeliac disease or for other conditions entered the study. The IFD and EMA-biopsy test showed a comparable, absolute sensibility and specificity for the diagnosis of coeliac disease both in clinically overt cases and in latent ones. EMA-biopsy test may by considered a very useful, simple test for diagnosing or excluding coeliac disease, especially when the clinical, serological and histological picture is not decisive.