Background: Type 1 diabetes mellitus (T1DM) is a common endocrine disorder associated with aberrant immune responses to specific β-cell auto-antigens. Markers of the process are various including auto-antibodies to glutamic acid decarboxylase (GADA) and to islet cell (IA-2). Other autoimmune diseases such as thyroid dysfunction are more common in T1DM. Autoimmune thyroid diseases are the most prevalent immunological diseases in patients with type 1 diabetes. Objectives: This study was planned to clarify the occurrence of autoimmune thyroid dysfunction and auto-antibodies in Egyptian patients with T1DM in patients without any history of thyroid disease and to assess its relation with diabetes-specific auto-antibodies. Methodology: This is a prospective case-controlled clinically-based study. Sixty patients diagnosed with diabetes type 1 according to WHO criteria for diagnosis of diabetes mellitus (DM) and 30 healthy controls matched for age, sex and body mass index (BMI) were recruited from the outpatient clinic of Endocrinology Department, Al-Zahraa Hospital, Al-Azhar University. All patients and controls were subjected to; Random blood glucose level, Glycated Hemoglobin (Hb A1c) assay level, Anti glutamic acid decarboxylase (anti-GAD), C-peptide level and Anti islet cell antigen (IA-2) auto antibodies, Serum free T3, free T4, TSH and Anti-Thyroid Autoantibodies (antithyoid peroxidase- TPO and anti-thyroglobulin-TG) were also done. Results: We reported that 45 patients (75.0%) were positive to autoantibody for GAD, 17 patients (28.3%) were positive for IA-2, 15 patients (25.0 %) for TPO, and 10 patients (16.66 %) were positive for TG-AB. All subjects with overt hypothyroidism (5 patients / 8.33%) had positive GAD and thyroid auto-antibodies, subclinical hypothyroidism (SCH) were reported in 15 patients (25%) and One subject only (1.67%) had clinical hyperthyroidism. Conclusions: We found a high prevalence of diabetes-specific auto-antibodies in T1DM patients. Subclinical thyroid dysfunction was evident in a considerable number of T1DM patients. These results indicate the importance of regular thyroid screening in T1DM patients.