OBJECTIVE: To assess the value of constructive interference in steady-state, three-dimensional, Fourier transformation (CISS) magnetic resonance imaging in the endoscopic management of hydrocephalus and intracranial cysts. METHODS: CISS imaging and T2-weighted imaging were performed for 14 consecutive patients before and after fenestration procedures, using a flexible endoscope, to treat loculated or multiloculated hydrocephalus (4 patients), aqueductal stenosis or obstruction (4 patients), arachnoid cysts (4 patients), a cyst of the velum interpositum (1 patient), or an ependymal cyst (1 patient). Fifteen fenestration procedures were performed, including one reoperation. RESULTS: Preoperative CISS imaging demonstrated intracystic intraventricular septa not observed with conventional T2-weighted imaging for 11 of 15 procedures and provided better brain tissue/cerebrospinal fluid contrast, allowing better understanding of the cause of hydrocephalus and the nature of the cysts. CISS imaging and T2-weighted imaging were equally useful for monitoring postoperative changes in the sizes of ventricles or cysts and the presence of flow voids after third ventriculostomies. However, only CISS imaging clearly demonstrated the site of fenestration for six of the nine patients who underwent fenestration procedures. CONCLUSION: CISS imaging provides excellent cerebrospinal fluid/brain tissue contrast, allowing detailed study of the anatomic features of the ventricular system and cystic lesions. CISS imaging is valuable for both preoperative decision-making and postoperative evaluation.