Rathke’s cleft cyst becomes symptomatic in a few cases. Increasing experience has identified previously unrecognized clinical effects including pituitary dysfunction. This study retrospectively investigated eight patients with Rathke’s cleft cyst manifesting as hyponatremia and treated surgically with histological confirmation to clarify the mechanism of hyponatremia. All patients suffered from physical symptoms caused by the hyponatremia. All patients underwent magnetic resonance (MR) imaging and screening of pituitary hormones in addition to cortisol and thyroid hormones. All patients had cysts of more than 10 mm in diameter and MR imaging frequently showed irregularly thickened cyst wall. Histological examination disclosed various phases of inflammation and significant fibrosis. Endocrinological examination showed low concentrations of both serum cortisol in all eight patients and urinary cortisol in six of six patients examined. The major cause of hyponatremia was hypocortisolemia, induced by damage to the anterior pituitary gland.