Magnetic resonance imaging techniques have been developed to enable imaging of the live rat brain with thin (1.2‐mm) slices and microscopic pixels (115 × 115 μm). Signal‐to‐noise ratios high enough to realize the microscopic resolution are obtained with of coils designed for the subject and through the use of three dimensional Fourier spin warp imaging. The technique yields 16 contiguous slices. Correlation with fixed pathologic specimens enables unequivocal identification of gray and white matter structures in the brain of a live 200‐g rat. Structures clearly visible in the MR images include Ammon's horn, the hypothalamus, corpus callosum and substantia nigra, as well as a number of brainstem nuclei. © 1987 Academic Press, Inc.