The advent of modern neuroimaging tools and methods has revolutionized the evaluation of the brain in neonates. The development of magnetic resonance (MR)-compatible monitoring tools and incubators has alleviated concerns regarding transportation of these unstable infants. The development of dedicated neonatal imaging coils has increased signal-to-noise ratios dramatically in images of the neonatal brain; this has made high-quality anatomic imaging, diffusion tensor imaging, and proton MR spectroscopy feasible in a normal imaging time. In centers that are equipped properly for neonatal MR imaging, MR is now unquestionably the study of choice for neonates who have encephalopathy or suspected brain injury. This article discusses the application of modern MR techniques to some of the causes of encephalopathy in neonates.