The present study aims to report on the correlation between the degree of negativity of anti-endomysial antibodies and anti-tissue transglutaminase antibodies in the IgA and IgG classes with regard to histological grade, in 44 newly diagnosed children with celiac disease (CD). Samples with negative antibodies, but a positive histology from a 5-year program searching for CD in the pediatric population were collected. A total of 4247 biopsy samples were used in this study. We documented that certain pediatric patients are seronegative, while the disease is active and the incidence of CD is higher than expected in the pediatric population. This is an important finding, which demonstrates the lack of association between autoantibodies and lesions, and justifies the use of biopsies for an accurate CD diagnosis and the importance of revising the diagnostic criteria in a clinical, endoscopic and serological context. We recommend a more active search for incidences of the disease in the pediatric population. Serological markers are not the main method for the diagnosis of CD as they are considered to only have a supporting role clinically. Biopsies of the small intestine are always necessary for the diagnosis of CD in these patients.