Introduction: Diabetes mellitus and thyroid dysfunction are common endocrine disorders encountered in clinical practice. Prevalence of thyroid dysfunction in type II diabetes mellitus have not been studied much. Objective: To determine the thyroid hormone profile and thyroid autoimmunity in patients with type 2 diabetes mellitus. Design: Cross sectional study. Setting: 116 patients with type 2 diabetes mellitus who attended the Diabetes clinic, Government Medical College, Kozhikode, Kerala during a period of 1 year was included in the study group. Results: Mean TSH levels were 6.39± 13.97 and 4.86 ± 10.93 among the diabetics and non-diabetics respectively, which was statistically significant (p value 0.018). Biochemical thyroid dysfunction was detected in 31.03 %(36) of the diabetic group, which was statistically significant (p value: 0.008).Of these 32 individuals were hypothyroid (p value: 0.008), of which 19 had subclinical and 13 had overt hypothyroidism.4 diabetic individuals were hyperthyroid, of which 3 had overt and 1 had subclinical hyperthyroidism; this was not statistically significant.37 % of the study group and 34 % of the control group were anti TPO antibody positive, but no statistical significance was detected (p value: 0.88). Conclusions: The prevalence of Thyroid dysfunction is common in Type 2 diabetics, subclinical hypothyroidism being most common.