Migraineurs have less volume in midbrain regions and show morphologic shape indentations in ventral pons and midbrain as well as right and left outward deformations in the lateral aspects of the pons and medulla. Migraineurs with more severe allodynia have less midbrain volume and migraineurs with lower heat pain thresholds have less volume in the cerebellar peduncles and medulla. Brainstem morphological alterations might reflect dysfunctional pain modulation in migraine.