Aim: Our aim was to compare the presence of various common viruses (rhinovirus, enterovirus, adenovirus, Epstein–Barr virus, cytomegalovirus, norovirus, parechovirus) in stool and nasal swab samples as well as virus‐specific antibodies in serum samples between children who developed coeliac disease and controls.

Methods: A case–control study was established based on the DIABIMMUNE Study cohorts. During the study, eight Estonian children and 21 Finnish children aged 1.5 years to five years developed coeliac disease and each was matched with a disease‐free control. Nasal swabs and stool samples were taken at the age of three to six months and the serum samples at the time of diagnosis.

Results: Rhinovirus ribonucleic acid was detected in the nasal swabs from five coeliac disease children, but none of the control children (p = 0.05). There were no statistically significant differences in the level of viral antibodies between cases and controls. Enterovirus immunoglobulin G class antibodies were found more frequently in the Estonian than in the Finnish children (63% versus 23%, p = 0.02).

Conclusion: This study did not find any marked overall differences in laboratory‐confirmed common viral infections between the children who developed coeliac disease and the controls. However, rhinovirus infections were detected slightly more often in those patients who developed coeliac disease.