The aim of the study was to evaluate the natural course and potential risk factors of autoimmune thyroiditis (AIT) and thyroid dysfunction, and their influences on growth and glycemic control in children and adolescents with type 1 diabetes mellitus (T1D). The study comprised 148 subjects (age range 1-21 years; males 51%) with T1D. During the interval of 12 years serum levels of thyroid peroxidase (anti-TPO) and thyroglobulin (anti-TG) autoantibodies, thyroid-stimulating hormone (TSH) and tyroksine (T4), were screened annually. Height, weight, body mass index (BMI), glycosylated hemoglobin (HbA1c), insulin dose and the number of severe hypoglycemic episodes, were recorded every 3 months. The mean follow-up was 7 +/- 4.1 years. Prevalence of AIT in subjects with T1D was 15.5%. It was significantly higher in girls (21.9% vs. 9.3%; p = 0.03). The mean age at AIT onset was 11.5 +/- 5.2 years. The mean interval between negative and positive AIT screening was 2.5 +/- 2.3 years. Cumulative incidence of AIT after 6 years of T1D duration was significantly higher in girls (30% vs. 15%; p = 0.03). Prevalence of hypothyroidism was 8.1% with no significant differences in sex distribution. Prevalence of hypothyroidism among subjects with elevated serum thyroid antibodies was 52.2% with significant male preponderance (85.7% vs. 37.5%; p = 0.005). There were no subjects who developed hypothyroidism in absence of thyroid antibodies. Cumulative incidence of hypothyroidism after 3 years from the moment of thyroid antibodies appearance was 55% with significant male preponderance (85% vs. 40%; p = 0.005). The mean interval between T1D onset and hypothyroidism development was 3.3 +/- 2.5 years, and between thyroid antibodies appearance and hypothyreoidism development was 1.7 +/- 1.2 years. The mean age at hypothyroidism onset was 12.7 +/- 5.3 years. There were no differences in growth and metabolic control between patients with and without AIT. The results of the present study confirmed frequent occurrence of AIT and thyroid dysfunction in subjects with T1D. The number of newly diagnosed subjects with AIT reached the peak at the age of puberty. Girls were significantly more predisposed to AIT at any age while amongst subjects with elevated thyroid antibodies boys developed hypothyroidism more frequently. Annual screening of thyroid antibodies in all patients with T1D is recommended, while serum TSH level should be measured in patients with detected thyroid antibodies.