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Background Coeliac disease is a wheat gluten and related prolamines-induced disease with a prevalence that may be underestimated in many geographical regions and populations. Aim To investigate the prevalence of coeliac disease in a population of schoolchildren of Estonia using tissue transglutaminase antibodies for screening. Subjects and methods The study was designed as cross-sectional. Serum samples from 1160 randomly selected schoolchildren (636 female and 564 male, aged 9 or 15 years) were studied using a novel tissue transglutaminase antibody immunoassay (EliA™ Celikey® IgA assay). Antibody-positive subjects were investigated for coeliac disease. Results A total of five subjects had antibodies. Four of them agreed for further investigations. By small-bowel biopsy they all were confirmed to have active coeliac disease, including three subjects with symptoms that were not considered by their family doctors. The prevalence of coeliac disease is at least 1 case per 290 (0.34% with CI 0.09–0.88%) in Estonia. It is much higher than that in our previous screening studies but is comparable with data from other European countries. Conclusion The prevalence of coeliac disease might have increased during the last decade in Estonia. This study clearly shows that the awareness of coeliac disease among physicians is low. Thus, there is a need for more epidemiological studies and education related to coeliac disease.