Cysts of the septum pellucidum (CSP) are usually asymptomatic; however, in some cases they can begin expanding and cause neurological deterioration. The mechanism leading to the formation of an expanding cyst of the septum pellucidum (ECSP) is not known. Based on observations made during endoscopic treatment of ECSP we analyzed intraoperative findings in respect to cyst formation mechanism and treatment prognosis. A group of 31 patients was studied. Only cases with bulging cyst walls occupying the frontal horns observed on imaging studies were included. The main symptom was a severe, intermittent headache. In three cases short term memory deficits were diagnosed. In one case papilloedema was observed. All patients underwent endoscopic fenestration of the ECSP. There were no cases of cyst reocclusion during a follow-up period of 1-14 years (mean 6.2 years). In 30 cases headaches resolved completely and in one case its intensity was significantly smaller. There was one case of postoperative hemiparesis. In all but two cases the thin, translucent region in the anterior part of the cyst floor was found. In the region small fissures and in three cases choroid plexus were observed. Endoscopic fenestration is the efficient treatment for ECSP. ECSP is formed on the basis of not completely closed, developmental communication of the cyst with other fluid spaces. The communication is opened by transient elevation of intraventricular pressure, and acts as a valve leading to fluid accumulation among the walls of the previously asymptomatic cavum septum pellucidum.