Hashimoto Thyroiditis is an autoimmune disease that results in destruction of the thyroid gland and gradual and progressive thyroid failure. The more commonly reported malignancies in patients with Hashimoto’s Thyroiditis have been lymphoma and papillary carcinoma. A prevalence of medullary carcinoma of only 0.35% has been reported in Hashimoto’s patients. We present a case of 42 year old female who presented with complaint of swelling in the neck associated with difficulty in swallowing and hoarseness of voice. Total thyroidectomy was done. Histopathological examination reveals co-existence of Hashimoto’s Thyroiditis with Medullary carcinoma, which is a rare presentation.