Methods: A case control study included 32 children with autoimmune thyroiditis and 32 healthy subjects with matching age and sex were included as a control group. Thorough history, examination, thyroid ultrasound, measurement of thyroid-stimulating hormone (TSH) and free thyroxine (FT4), as well as anti-thyroid peroxidase antibodies (TPOAb) and anti-thyroglobulin antibody (TgAb) were done in addition to assessment of malondialdehyde (MDA) and total antioxidant capacity (TAC) levels as an oxidative stress markers. Results: Overt hypothyroidism was detected in 23/32 while subclinical hypothyroidism was detected in 9/32 of the studied patients. Malondialdehyde levels were significantly elevated while total antioxidant capacity levels were significantly decreased in autoimmune thyroiditis patients compared with healthy controls. The difference was more evident in patients with overt hypothyroidism than those with subclinical hypothyroidism. We also observed a significant positive correlation between anti-thyroid peroxidase antibodies levels and age, TSH, malondialdehyde, thyroid volume and a negative correlation with total antioxidant capacity and thyroxine .