The presence of flexures between the mesencephalon, pons and medulla oblongata implies the definition of specific orientations of axial sections for each level of the brain stem. These axial sections have to be perpendicular to the axis of the corresponding segment. For the mesencephalon, we have defined an axis corresponding to a straight line of best fit to the mesencephalic anatomical axis; the whole of the rhombencephalon has been referred to an axis taken through the pons and the intracranial medulla that is tangential to the floor of the IV ventricle. Identical reference planes can be obtained in CT by programming, on the scout view of the skull, perpendicular sections of the clivus that allow the study of the axial aspect of the mesencephalon, with sections at - 7 degrees through Chamberlain's line for visualization of the same aspect of the rhombencephalon. We have thus defined the referential planes to analyse every level of the brain stem using reproducible axial sections, able to be applied to different patients as well as to different examining techniques (TDM, MRI).