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We set out to introduce serum markers into the diagnosis of coeliac disease as a substitute or supplement to small intestinal mucosa biopsy. At the Paediatrics Department of the Maribor Teaching Hospital, determinations of antigliadin (AGA-IgA and AGA-IgG) and antiendomysial antibodies are carried out in to asses the reliability of these coeliac disease markers in indicating the state of small intestinal mucosa. We examined the records of 74 children in which small intestinal mucosa biopsy had been performed and antigliadin as well as antiendomysial antibodies had been determined at the same time. According to the degree of small intestinal mucosa atrophy they were assigned to the following three groups: 1. 24 children with normal small intestinal mucosa, 2. 30 children with partial or moderate atrophy and 3. 20 children with total atrophy of the small intestinal mucosa. For all markers the connection with the degree of small intestinal mucosa atrophy was proven (p < 0.0001 in all markers). The reliability of negative markers as indicators of healthy mucosa lay between 44.4% and 57.1% for all markers and combinations. The reliability of positive serum markers was absolute (100%) for the following markers: AGA-IgA, for the combinations AGA-IgA + AGA-IgG and AGA-IgA + EMA as well as for the combination of all three markers. A positive antiendomysial marker was reliable in 95.2% and AGA-IgG in 78.6%. We believe that in children in which all three markers of coeliac disease are positive, it would be reasonable to contemplate whether small intestinal mucosa biopsy is justified.