Background Elevated titers of antibodies against different herpes virus antigens have been reported in some immunodeficient and systemic autoimmune disorders. Objective To examine if Herpes Simplex Virus (HSV), Epstein-Barr virus (EBV), and cytomegalovirus (CMV) IgG and IgM antibodies are detected more frequently in children with autoimmune thyroid disease (AITD) compared to controls. Subjects and methods Thirty-four children with AITD, aged 9.62 ± 2.35 years, and 31 matched controls, aged 9.24 ± 2.98 years, were studied. Results The percentage of EBV IgG+ children with AITD was statistically higher than the percentage of EBV IgG+ controls (82.35% versus 51.61%, P = 0.008). The percentage of EBV IgG+ children with AITD and hypothyroidism was statistically higher than the percentage of EBV IgG+ children with AITD, without hypothyroidism (100% versus 70%, P = 0.024). No other statistically significant differences were observed in HSV−1+2, and CMV IgG or IgM antibodies between the subgroups of children studied. Conclusions EBV seroprevalence is higher in children with AITD compared to controls and the underlying pathology remains to be elucidated.