We have performed a prospective study of the use of magnetic resonance (MR) imaging in 14 patients undergoing neuro-endoscopic third ventriculostomy. MR imaging was undertaken prior to the endoscopy and serial studies were carried out after the procedure. MR imaging provides important information concerning the morphology of the third ventricle and allows the identification of an appropriate puncture site in the floor of the third ventricle. In particular, the relationship of the third ventricular floor to the basilar artery is well demonstrated. Following an endoscopic septostomy, MR imaging allows visualisation of any change in ventricular size. A cerebro-spinal fluid (CSF) flow void in the anterior inferior third ventricle, sometimes extending into the suprasellar cisterns was frequently demonstrated and this was found to be a more constant feature than reduction in ventricular size. MR imaging provides an indispensable tool for both planning and follow-up of endoscopic third ventriculostomy.