Background: Vitamin D deficiency or insufficiency may play a role in the pathogenesis of certain autoimmune diseases. Aim: To measure vitamin D levels in children with Hashimoto’s thyroiditis (HT) (either with subclinical or marked hypothyroidism) and in healthy controls. Material and Methods: We included 68 children with HT aged 12 ± 4 years (39 females) from a pediatric outpatient clinic and 68 healthy children aged 10 ± 4 years (37 females). Calcium metabolism parameters, thyroid function tests and anti-thyroid peroxidase (anti-TPO), anti-thyroglobulin (anti-TG) and 25 hydroxy vitamin D (25OHD) levels were measured. Results: Patients were older than controls but well matched by gender distribution. Mean 25OHD levels were significantly lower in HT patients than controls (16.8 ± 9.3 and 24.1 ± 9.4 ng/mL respectively, P < 0.01). Frequency of vitamin D deficiency was 76 and 35% in HT patients and controls, respectively (P < 0.001). Conclusions: Vitamin D deficiency is more common in children with HT than healthy controls.