Prolonged juvenile hypothyroidism results in a permanent loss in height that is related to the duration of thyroxine deficiency before adequate thyroxine replacement treatment. A 13 year old girl with severe juvenile hypothyroidism was studied prospectively. She had an undetectable serum thyroxine concentration, a height SD score of -6.6 SD, and a bone age of 5.8 years. The enlarged pituitary gland involuted with thyroxine treatment to produce an empty sella. In addition to thyroxine the girl was treated with a gonadotrophin releasing hormone agonist to avoid the progression of puberty for 18 months and with growth hormone to achieve normal adult height.