PURPOSE: Rathke cleft cysts (RCC) usually are asymptomatic and can be observed via the use of conservative methods. Some patients with RCCs, however, have severe headaches even if they are small enough to be confined to the sella, and these small RCCs seldom have been discussed. This study presents an investigation into clinical characteristics of small RCCs associated with severe headaches, demonstrating efficacy and safety of endoscopic transsphenoidal surgery (ETSS) to relieve headaches. METHODS:In this study, 13 patients with small RCCs (maximum diameter < 10 mm) who presented with headaches and were treated by ETSS at our institute from 2009 to 2014 were recruited. These RCCs were treated Headache Impact Test-6 (HIT-6) score was calculated both pre-and postoperatively to evaluate headache severity. RESULTS: All patients complained of severe headaches, which disturbed their daily life. Most headaches were nonpulsating and localized in the frontal area. Characteristically, 6 patients (46%) experienced severe headaches with sudden onset that continued chronically. HIT-6 score was 64 on average, meaning headaches affected daily life severely. After surgical decompression of the cyst, headache in all of the patients improved dramatically and HIT-6 score decreased significantly to 37, suggesting that headaches were diminished. No newly developed deficiencies of the anterior pituitary lobe function were detected. Postoperative occurrence of diabetes insipidus was found in 2 patients, both of which were transient. No recurring cysts were found. CONCLUSIONS: Severe headaches can develop from small RCCs. In the present study, ETSS was performed on such patients effectively and safely to relieve their headaches.