Abstract Introduction Celiac disease (CeD) may cause changes throughout the gastrointestinal tract. It is not known whether the oesophageal mucosa is involved in CeD. The purpose of this prospective study was to study the mucosal changes in oesophagus in children with CeD. Materials & Methods The mucosal changes in the esophagus was prospectively investigated in 126 children with CeD during 192 upper GI endoscopies performed to obtain duodenal biopsy specimens and was compared with findings in 49 children who underwent endoscopy for upper GI complaints without CeD (non-CeD patients) during one year. Children were diagnosed as cases of CeD based on the modified ESPGHAN criteria and positive serology. Duodenal histologic lesions were classified as proposed by our group. Results The mean age of CeD children (M:F::71:55) at presentation was 6.7 + 3.3 years. 54/126 (42.9%) of CeD and 23/49 (46.9%) of non-CeD patients showed normal oesophageal mucosa. The prevalence of lymphocytic oesophagitis (LyE) was higher in CeD (11.9%) than non-CeD (2.1%) patients. The prevalence of oeosinophilic oesophagitis, follicular oesophagitis, reflux oesophagitis and non-specific oesophageal mucosal changes were similar in both groups. All but one child with LyE showed classic duodenal histologic lesion. Conclusions Our findings showed that the oesophageal mucosa can be damaged in CeD patients and that the prevalence of LyE is higher with CeD. Awareness of potential coexistence of oesophageal lesions in CeD should promote optimal diagnosis of these conditions. Routine oesophageal biopsies may be warranted when investigating for CeD.