This review article draws upon the extensive comparative studies between computed tomography (CT) and magnetic resonance (MR) imaging in the central nervous system. The comparisons and clinical applications of the imaging modalities are discussed under specific regions. Whenever possible, actual statistics from the comparative studies are cited. The results show a distinct advantage of MR over CT in the posterior fossa, the perisellar region and diseases involving the leptemeninges and white matter. Cranial nerves, which are usually not seen on CT, are much better appreciated on MR imaging. Because of its multiplanar capability, lesions adjacent to the skull base are better demonstrated on coronal and sagittal planes. CT is able to show calcification, subarachnoid haemorrhage and acute haematoma better than MR. In acutely-ill patients with cerebro-vascular accident and head trauma, CT is also found to be more useful than MR. This article also gives a suggested guideline of the clinical applications of MR as a primary or complementary imaging modality.