Magnetic resonance imaging reveals the anatomy of the pituitary and hypothalamus with unique detail. The clinical and biochemical investigation of short stature in childhood may be difficult and complex; magnetic resonance imaging of the pituitary is a non-invasive technique which can help to clarify the diagnosis of growth hormone insufficiency and to determine its cause. Most cases of growth hormone insufficiency have previously been considered to be idiopathic; in about 60% of these children, magnetic resonance imaging shows a characteristic structural abnormality which has been termed pituitary stalk interruption syndrome. The most important role of magnetic resonance imaging is in the diagnosis of destructive lesions of the hypothalamic-pituitary axis which may initially present with growth failure.