The aim was to determine the prevalence of coeliac disease (CD) in paediatric patients with migraine. Serum tissue transglutaminase IgA (tTGA) antibodies and IgA concentrations were measured in 73 patients with migraine (age range 6–17 years) and the control group (n = 147). Patients having positive tTGA antibodies underwent duedonal biopsy. Four patients (5.5%) from the study group and one (0.6%) from the control group had positive tTGA antibody titres (P < 0.05). Three patients with migraine had normal duedonal histology and were considered as potential CD. One patient from the study group and one from the control group declined to have biopsy. tTGA antibody is considered as a reliable indicator for the presence of CD. However, some patients with positive antibodies may have normal biopsy initially and are classified as having potential CD. Our finding of a higher prevalance of tTGA antibodies in paediatric migraine patients suggests that an association between migraine and CD might exist.