Children with untreated coeliac disease (CD) may develop enamel defects. Moreover, children with untreated CD have increased serum levels of gliadin reactive IgG, which may cross-react to amelogenin. The aim of this study was to investigate reactivity of anti-gliadin IgA and IgG to amelogenin in children with untreated CD. Blood samples from patients with CD (n = 75) and from disease controls (n = 24) were analysed for IgA and IgG reactivities to amelogenin (Emdogain) and to gliadin by ELISA. Whereas children with CD had statistically significantly higher serum levels of anti-amelogenin IgA, only those with the most severe CD (Marsh 3c) had significantly higher anti-amelogenin IgG immune reactivity than the disease controls. Western blotting confirmed that the IgA and IgG immune reactivity was to the amelogenin-specific bands in Emdogain and to a 22-kDa human recombinant amelogenin. Cross-inhibition studies revealed that the anti-amelogenin immune reactivity was not only caused by anti-gliadin cross-reactivity but also included amelogenin selective immune reactivity. Some controls had high levels of anti-amelogenin IgA and IgG, similar to children with CD. Thus, anti-amelogenin IgA and IgG may not only be involved in the aetiology of CD-associated enamel defects but may also interfere with enamel maturation in non-coeliac children.