The neural mechanisms responsible for the initiation and expression of migraines remain unknown. Though there is growing evidence of changes in brainstem anatomy and function between attacks, very little is known about brainstem function and structure in the period immediately prior to a migraine. The aim of this investigation is to use brainstem-specific analyses of diffusion weighted images to determine if the brainstem pain processing regions display altered structure in individuals with migraine across the migraine cycle, and in particular immediately prior to a migraine. Diffusion tensor images (29 controls, 36 migraineurs) were used to assess brainstem anatomy in migraineurs compared with controls. We found that during the interictal phase, migraineurs displayed greater mean diffusivity in the region of the spinal trigeminal nucleus, dorsomedial/dorsolateral pons and midbrain periaqueductal gray matter/cuneiform nucleus. Remarkably, the mean diffusivity returned to controls levels during the 24-hour period immediately prior to a migraine, only to increase again within the three following days. Additionally, fractional anisotropy was significantly elevated in the region of the medial lemniscus/ventral trigeminal thalamic tract in migraineurs compared with controls over the entire migraine cycle. These data show that regional brainstem anatomy changes over the migraine cycle, with specific anatomical changes occurring in the 24 hours prior to onset. These changes may contribute to the activation of the ascending trigeminal pathway by either an increase in basal traffic or by sensitising the trigeminal nuclei to external triggers, with activation ultimately resulting in perception of head pain during a migraine attack. It has been hypothesised that modulation of brainstem pain pathways may be critical for the initiation of migraine attacks. There is some evidence that altered brainstem function, possibly involving increased astrocyte activation, occurs immediately prior to a migraine attack. We sought to obtain evidence to support this theory. Using diffusion tensor imaging, we found that immediately prior to a migraine, mean diffusivity decreased in the spinal trigeminal nucleus, dorsomedial/dorsolateral pons and midbrain periaqueductal gray matter/nucleus cuneiform. Mean diffusivity then increased again immediately following the migraine attack. Decreased mean diffusivity before a migraine is consistent with increased astrocyte activation, since astrocyte processes enlarge during activation. These changes may underlie changes in brainstem function that are essential for the generation of a migraine.