Background: Polycystic ovarian syndrome (PCOS) and thyroid disorders are the most common endocrine disorders in women. Evidently, the involvement of polycystic ovarian syndrome (PCOS) and thyroid autoimmunity triggering thyroid disorders has not yet occurred. Objective: The aim was to assess serum free tri-iodothyronine (FT3), free thyroxin (FT4) and anti-thyroglobulin antibodies among polycystic ovary syndrome Sudanese patients. Materials and methods: Fifty Sudanese patients diagnosed with PCOS and 50 healthy age matched females were recruited in this cross-sectional controlled study. Serum FT3 and FT4 were measured by an immunoassay analyzer and serum anti-thyroglobulin antibodies were measured using ELISA. The data was then analyzed using the SPSS. Results: The results showed a significant increase in serum FT3 and anti-thyroglobulin antibodies and there was no statistical difference in PCOS serum FT4 levels compared to the control group. The results revealed no correlation between levels of FT3, FT4 and anti-thyroglobulin antibodies with age; also there were no correlation between levels of FT3 and FT4 with BMI while there was a positive correlation between anti-thyroglobulin antibodies levels and BMI. Conclusion: Patients with PCOS had elevated FT3 and antithyroglobulin. Therefore, the assessment of thyroid autoantibody with thyroid hormones in patients with PCOS should be investigated.