Introduction: India has the higher prevalence of prediabetes, diabetes and hypothyroidism. Subclinical Hypothyroidism (SH) is more prevalent in the females than in the males. Studies have shown the elevated HbA1c in the non-diabetic hypothyroid patients. SH is defined by normal serum triiodothyronine (T-3), thyroxine (T-4) levels and serum Thyroid Stimulating Hormone (TSH) level falling between 4.2 to 10 mU/ L. Aim: To study the HbA1c level in the non-diabetic subclinical hypothyroid patients and to compare the HbA1c level with the controls. Materials and Methods: This case-control study was conducted on 200 subjects. A total of 100 subjects of the subclinical hypothyroidism without diabetes were selected on the basis of the serum TSH (>4.2 to < 10 mU/L), Fasting Blood Sugar (FBS) (< 110 mg/dl) level and another 100 age and sex matched normal healthy individuals were selected as the control. The HbA1c levels were measured using Immunoturbidimetry method in the Cobas Integra 400 plus. An independent t-test is applied to find out the statistically significant difference in the level of HbA1c in the case and the control groups. Results: Subjects with the non-diabetic subclinical hypothyroidism had a significant higher level (5.70 +/- 0.35 %) of the HbA1c than the controls (5.26 +/- 0.17 %) (p < 0.0001). There was no significant difference between the cases and the controls for the age, sex, FBS, vitamin D-3, Haemoglobin (Hb), serum T-3 and serum T-4 levels. Conclusion: Our data suggest that the non-diabetic subjects with subclinical hypothyroidism show misleadingly high levels of the HbA1c. Therefore, the effect of altered levels of the serum TSH on the HbA1c must be considered when interpreting the HbA1c for the diagnosis of diabetes in the subclinical hypothyroid patients.