Introduction: Thyroid dysfunction is among the most common autoimmune disorders in women of reproductive age. Previous studies have shown the association between autoimmune thyroid disease (AITD) and infertility. Anti-Müllerian hormone (AMH) is secreted by granulosa cells and is a useful marker for assessment of ovarian reserve. In the present study, we sought to evaluate the ovarian reserves of women with autoimmune thyroid disorder by measurement of AMH values. Material and methods: This prospective study included women with newly diagnosed AITD aged between 20 and 40 years. Patients were divided into three groups: Subclinical hypothyroidism (SCH, n = 21), overt hypothyroidism (OH, n = 21) and controls (CG, n = 32). Study parameters included serum free T4, free T3, thyroid-stimulating hormone, anti-thyroglobulin, anti-thyroid peroxidase antibodies, follicle-stimulating hormone, luteinizing hormone, estradiol and AMH concentrations measured in the early follicular phase. Antral follicle count (AFC) was assessed with ultrasound. Body mass index (BMI) and waist circumference of the patients were noted. Results: No significant difference was found among SCH, OH and CG in regard to ovarian reserves measured by AMH values (p = 0.19) and AFC (p = 0.80). A significant negative correlation was found between AMH and BMI (r = -0.382, p = 0.001). Anti-Müllerian hormone and waist circumference (r = -0.330, p = 0.004) were also negatively correlated. Conclusions: Although AMH values were not significantly different among groups, AMH values were lower in OH and SCH patients, indicating a possible need for close monitoring of these patients.