Agenesis (complete non formation) of human organs or glands is known since antiquity for example asplenia (spleenic agenesis), gall bladder agenesis, renal agenesis and so on. Endocrine glands like adrenals and thyroid are no exception to agenesis. Thyroid is the first endocrine gland to develop and is not uncommonly affected with congenital abnormalities. Commonest is left lobar hemi-agenesis. However, only one case of bilobar thyroid agenesis (BTA) has been reported in the literature. We report a case of BTA with adenomatous Isthmus and sub clinical hypothyroidism in a 13 year old girl who presented with midline thyroid nodule. FNAC was suggestive of colloid nodule with cystic degeneration. Preoperatively hypothyroidism was corrected. At surgery, entire isthmus was found to be replaced by a large cyst and both lobes of the thyroid were absent. So, Isthmusectomy amounting to total thyroidectomy was done and she was put on thyroxine replacement therapy. Preoperative diagnosis of BTA is difficult even if patient develops nodule or becomes symptomatic. Many cases go unnoticed or detected only intra operatively; and they require life long thyroxine replacement therapy.