Magnetic resonance imaging (MRI) is a valuable, noninvasive tool for understanding structural abnormalities in the brain. The M.I.N.D. Institute at UC Davis has developed a protocol utilizing MRI to investigate anatomical differences in the post-mortem brain by applying a proton density weighted imaging sequence for optimal differences in image intensity (contrast) between gray and white matter. Images of the brain obtained prior to distribution of tissue and further neuropathological examination provide a record of how the brain appeared prior to tissue processing. The virtual representation of the whole brain can also be subjected to additional analyses, such as measuring the volume of brain regions or area of the cortical surface. We describe our procedures for carrying out post-mortem MRI of the human brain.