Aim We aimed to analyse the influence of the COVID-19 pandemic on the frequency and clinical presentation of celiac disease. Methods The study included the patients with celiac disease since January 2008. They were divided into 2 groups (diagnosed in pre-pandemic [January 2008 and February 2020] [n = 148] and in pandemic period [March 2020 and June 2021] [n = 47]). Clinical and histological findings were compared between groups. Additionally, data about severe acute respiratory syndrome coronavirus 2 infection were obtained in subgroup patients (n = 22) with celiac disease diagnosed during pandemic period. Results The number of patients per year (12.1-37.6) and the percentage of patients who were diagnosed with celiac disease/total endoscopy were increased during the pandemic period (2.2% vs. 10%, p < 0.00001). The association of celiac disease with type 1 diabetes mellitus was significantly high in pandemic period (4% vs. 17%, p = 0.002). Frequency of moderate-severe mucosal lesions was low in pandemic period (42.4% vs. 81.7%, p = 0.0001). Clinical and laboratory markers for the past severe acute respiratory syndrome coronavirus 2 infection were found in 36.3% of patients diagnosed during the pandemic period. Conclusion It seems that the frequency of celiac disease and its association with type 1 diabetes mellitus is increased during the COVID-19 pandemic in children.