We report a rare case of glomerulocystic kidney disease (GCKD) with congenital hypothyroidism. A gigantic abdominal mass was noted at birth. There was no family history of renal cystic disease. Ultrasonography revealed diffuse granular cysts in the markedly enlarged kidneys. Blood examination showed moderate renal failure and hypothyroidism. Bilateral nephrectomy was conducted at 47 days of age to relieve respiratory failure and severe abdominal distention caused by the growing cystic kidneys. Histological findings of the kidney showed numerous glomerular cysts without renal dysplasia. There were no other malformations. These findings were compatible with GCKD.