We report a girl with Down syndrome who was diagnosed with congenital hypothyroidism in the newborn period due to left thyroid hemiagenesis. Unexpectedly, her hypothyroidism resolved at the age of 3 years. After being off thyroid hormone replacement for 7 years and having normal thyroid function, she developed Graves' disease. Although Graves' disease in association with thyroid hemiagenesis has previously been reported, this represents the youngest patient in whom this scenario has been described. Issues pertaining to thyroid hemiagenesis, autoimmune hyperthyroidism, and thyroid disease in children with Down's syndrome are discussed.