OBJECTIVE: Intraventricular virtual MR endoscopic imaging of the foramen of Monro region by using three-dimensional Fourier transformation constructive interference in steady state (3DFT-CISS) magnetic resonance imaging in a patient with a unilateral congenital obstruction of the foramen of Monro by a transparent membranous septum was performed to enhance the orientation, achieve a better understanding of the pathology, and plan the surgical intervention in an endoscopic approach to the lateral ventricles. METHODS: 3DFT-CISS sequences and virtual MR endoscopic imaging were performed in a patient before and after endoscopic fenestration procedures, to communicate the lateral ventricle to the third ventricle for the treatment of unilateral ventricular enlargement. RESULTS: Preoperative 3DFT-CISS imaging demonstrated unilateral membranous septa in the localization of the left foramen of Monro which were not observed with routine T2-weighted imaging. 3DFT-CISS imaging and T2-weighted imaging were equally useful for monitoring postoperative changes in the size of the ventricles or cysts and the presence of flow voids after fenestration procedures, but only 3DFT-CISS imaging clearly demonstrated the area of fenestration. CONCLUSION: Virtual MR endoscopy by using 3DFT-CISS sequences is a feasible method in the planning of intraventricular real-time endoscopic surgery, for the enhancement of orientation in a surgical field, and to achieve a better understanding of the pathology.