Coeliac disease (CD) is an immune-mediated inflammatory disease triggered by dietary gluten and related proteins in genetically predisposed individuals. Point-of-care (POC) methods are non-invasive and easily performed tests, which could help to reduce the diagnostic delay of CD. The aim of our study was to determine the prevalence of CD using rapid POC test in first-grade schoolchildren in Zagreb, Croatia. A rapid qualitative immunoassay POC test designed for detection of immunoglobulin (Ig) A and IgG deamidated gliadin antibodies (DGP), as well as total IgA (to identify IgA deficient patients) in whole blood, was used to test healthy children on gluten containing diet. Out of 1404 tested children (51% female), 85 (6.05%) had a positive rapid POC test result and were referred to paediatric gastroenterologist. Finally, 7 children were diagnosed with CD (0.5%). There was no significant difference in children with CD and children with positive POC but negative serology in sex, BMI, or symptoms. However, children diagnosed with CD complained of abdominal pain significantly more often. The prevalence of CD in first-grade schoolchildren was 1:200 (0.5%), higher than in previous studies performed in Croatia. The results imply the possible benefit of IgA and IgG DGP-based POC tests in population screening.