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Celiac disease (CD) has a high prevalence but remains largely underdiagnosed. Although extensive studies have confirmed that children with CD do not have an increased risk of severe COVID-19, public health regulations associated with the SARS-CoV-2 pandemic may have exacerbated this problem. The aim of this study was to assess the effect of SARS-CoV-2 on the number of new-onset CD cases. Additionally, the role of SARS-CoV-2 in autoimmune diseases and its influence on clinical practice in pediatric gastroenterology were briefly reviewed. We described the data from the hospital electronic registry of new-onset CD, during the COVID-19 pandemic and 2 years before. A total of 423 children were diagnosed with CD between March 2018 and February 2022: 228 in the 2-year pre-COVID-19 period and 195 during the pandemic. The number of patients during the COVID-19 pandemic was 14.5% lower than in the previous years. The quarterly comparison of CD diagnoses showed a reduction in all quarters. A reduction in diagnoses during the lockdown and in the following months was evident and not compensated thereafter. This is the first study to evaluate the impact of SARS-CoV-2 on the diagnosis of CD in children. Further studies are necessary to improve the system of biopsy-sparing diagnosis and to evaluate the effect of the diagnostic delay. Special attention should be given to the implementation of telemedicine services.