A prospective study compared the abilities of high-resolution computed tomography (HRCT) and magnetic resonance (MR) imaging in detection and evaluation of central nervous system disease in neurologically symptomatic patients with acquired immunodeficiency syndrome (AIDS). Eighteen CT scans and 19 MR images in 14 patients were compared. HRCT images with contrast material enhancement were superior to unenhanced 0.35-T MR images for differentiating a lesion from surrounding edema, discriminating between lesions in close proximity, locating lesions for biopsy, judging lesion activity, detecting small cortical lesions with minimal edema, and spatial resolution. MR imaging was superior to CT scanning in evaluation of white-matter lesions and detection of small lesions surrounded by edema. MR imaging exhibited higher contrast resolution and greater sensitivity. Complementary uses of MR and CT imaging are suggested.