Autoimmune thyroid diseases are multifaceted conditions in which the thyroid gland is infiltrated by lymphocytes, resulting in the production of thyroid-specific auto-antibodies against thyroid peroxidase (TPOAb) and thyroglobulin (TGAb). Iron deficiency is a common nutritional deficiency and has multiple adverse effects on thyroid metabolism. The association between iron status and thyroid autoimmunity has not been well-evaluated. This retrospective study aimed to determine whether the frequency of iron deficiency was higher in patients with thyroid autoimmunity than in healthy individuals with negative thyroid autoantibodies. One-hundred-and-eighty female patients with positive thyroid auto-antibodies and 81 healthy controls were involved in the study. Hemoglobin, hematocrit, mean corpuscular volume (MCV), iron, thyrotropin (TSH), TPOAb, TGAb, free-T4, vitamin B12, ferritin and transferrin saturation (TS) were recorded. TSH, TPOAb and TGAb levels were significantly higher, while hemoglobin, hematocrit, MCV, ferritin, iron and TS were significantly lower in the patient group (all, p<0.05). Patients with thyroid autoimmunity had significantly higher frequency of lower levels of hemoglobin, iron, ferritin, MCV and TS than healthy controls (all, p<0.005). Correlations were found inversely between TPOAb and serum ferritin, iron, and TS levels, and also positively between TGAb and creatinine levels in the patient group. In conclusion, we found increased prevalence of iron deficiency in female patients with thyroid autoimmunity. Patients with autoimmune thyroid diseases were found to be at higher risk of iron deficiency development.