BACKGROUND HbA1c is an important parameter in diagnosis of diabetes. However, many other factors can independently influence HbA1c levels. The present study was aimed to determine the affect hypothyroidism on HbA1c level. MATERIALS AND METHODS 50 individuals were selected for this study who attended Al-Ameen Medical College Hospital from December 2014 to October 2016 after applying inclusion and exclusion criteria. 25 served as cases and other 25 as control. Relevant investigations were carried out. Thyroid hormone replacement was initiated in 25 hypothyroid cases and they were again reviewed after 6 to 12 weeks. TSH and HbA1c along with other relevant investigations were repeated. RESULTS A total of 25 cases and 25 controls were studied with comparable mean age in both groups. The mean HbA1c in hypothyroid cases is 5.58% and in controls is 5.4%, the difference between the means was mild but statistically not significant. The mean TSH in cases was 89.6 and in controls was 2.28. The difference between the means was statistically significant (p < 0.001). All the 25 cases were evaluated again on second visit. There was a statistically significant reduction in mean TSH (p= < 0.001) and HbA1c (p= 0.033) after thyroid replacement therapy when compared to pretreatment values in cases. CONCLUSION HbA1c and TSH levels were found to be high in non-diabetic hypothyroid subjects compared normal controls and there was drop in levels of HbA1c and TSH after initiation of thyroid hormone replacement.