Type 1 diabetes mellitus is frequently associated with autoimmune thyroid disease (ATD).Genetic susceptibility for autoantibody formation in association with ATD and type 1 diabetes mellitus has been described with varying frequencies, but there is still debate about its prevailing situation in Iran. We have therefore investigated the prevalence of anti-thyroid peroxidase (anti-TPO) and anti thyroglubolin (Anti TG) antibodies in type 1 diabetic patients, and compared the effect of age and sex on the thyroid autoimmunity in patients with type 1 diabetes mellitus in Iran.Ninety one subjects with type 1 diabetes mellitus and one hundred and sixty three unrelated normal controls under the age of thirty years were recruited for the detection of anti-TPO and anti-TG. Radio Immuno Assay and chemiluminescence methods were used for anti-TPO and anti-TG detection respectively.Among 91 type 1 diabetic patients, 36 (39.6%) were positive for anti-TPO and 27(30%) were positive for antiTG. Anti-TPO antibodies were detected only in 6.7% of control group. Comparing with those without thyroid autoimmunity, there was a female preponderance for the type 1 diabetic patients with thyroid autoimmunity (female: male, 28:14 vs. 28:20 respectively). Among the type 1 diabetic patients those with thyroid autoimmunity, tended to be older (p: 0.04) and to have higher TSH concentration (p: 0.03). Patients with high anti-TPO levels had longer duration of diabetes (P: 0.02).The presence of anti-TPO in 39.6% of our type 1 diabetic patients comparing with 8.5% of normal subjects confirmed the strong association of ATD and type 1 diabetes mellitus.