The lower brainstem and cervical spinal cord from an ordinarily treated case of Chiari Type I hindbrain hernia associated with syringomyelia was examined using high-resolution magnetic resonance microscopy and standard neuropathological techniques. Magnetic resonance microscopy allows total screening and visualizes the disturbed internal and external microanatomy in the three orthogonal planes with the resolution of low-power optical microscopy. An additional advantage is the in situ visualization of the shunts. Afterwards the intact specimen is still available for microscopic examination. Part of the deformation of the medulla is caused by chronic tonsillar compression and molding inside the foramen magnum. Other anomalies, such as atrophy caused by demyelination, elongation, and unusual disturbances at the level of the trigeminal and solitary nuclear complexes contribute to the deformation. At the level of the syrinx-free upper part of the cervical cord, anomalies of the dorsal root and the dorsal horn are demonstrated.