© 2018, Universa Press. All rights reserved.Backgrounds/Aims: Although the presence of autoimmune thyroiditis (AT) in celiac disease (CD) has been well documented among adults, CD in AT has been less reported in children. We aimed to investigate the frequency of CD in children with AT. Materials and Methods: This prospective study was carried out from October 2015 to August 2016 and included 66 patients with AT. Firstly, total IgA and tissue transglutaminase antibody (tTG) IgA levels were measured. Those with increased level of tTG IgA were tested for anti-endomysium IgA antibodies (EMA). Patients with positive EMA underwent gastroduodenoscopy for a definitive diagnosis of CD. Results: Sixty-six patients with AT (52 female) with mean age of 14.68 ± 3.18 years were enrolled. IgA deficiency was found in four patients. Only three of 66 patients (4.5%) were positive for tTG IgA. Patients positive for tTG IgA were then tested for EMA, and only one of them (1.5%) had positive EMA antibodies. Gastroduodenoscopy was performed in this patient. The result of pathological investigation was compatible with CD. Furthermore, one patient with AT had been diagnosed with CD previously. Conclusions: Two (3.0%) of 66 patients with AT were found to have CD. According to the results, we assume that there is a close relationship between CD and AT disease. However, there is a need for multicentric, prospective studies that would support our findings.