Background: Polycystic ovary syndrome (PCOS) is the most common endocrinopathy seen in reproductive age women. Recent literature suggests an increase in the incidence of thyroid disorders in females with polycystic ovary syndrome. The aim of this study is to evaluate the occurrence of thyroid dysfunction in subjects with polycystic ovarian syndrome as compared to controls of same age group. The study was a case control study conducted on 90 women, in whom 60 women were diagnosed with PCOS euthyroid and PCOS hypothyroid each and 30 normal healthy women with regular menstrual cycles as the control group within the age group of 20 to 40 years. The study was conducted at the department of Physiology, Kakatiya medical college, Warangal. The study revealed that the thyroid dysfunction was observed in the PCOS groups when compared to the control group. The PCOS hypothyroid women had significantly increased levels of TSH levels when compared to the PCOS euthyroid and control women. The T3 levels were significantly reduced in the PCOS hypothyroid women when compared to PCOS euthyroid and control groups. T4 levels were similar in all the groups. The FSH levels did not show any significant difference between the PCOS euthyroid and PCOS hypothyroid groups, but LH levels showed statistically significant difference between the PCOS euthyroid and PCOS hypothyroid groups. There was an association between the PCOS and the thyroid dysfunction as the TSH levels of the PCOS euthyroid were significantly higher than the control groups and very high in the PCOS hypothyroid groups.