Migraine is a complex disabling disease influenced mainly by age and gender during the life span. Neuroendocrine events related to reproductive stages and to the menstrual cycle may cause significant change in the clinical pattern of migraine over time, as a consequence of failure in adaptation higher in women than in men. Indeed, the individual threshold of vulnerability to manifest migraine is modulated by hormonal fluctuations naturally occurring throughout the menstrual cycle and at the time of reproductive transitions. In the present short review, the role of endogenous estrogen at the level of brain circuitries which are involved in multiple cellular, neurochemical and neurophysiological processes associated with migraine will be summarized in the context of reproductive milestones. In addition, some clues to recognize hormonally sensitive women on the basis of their migraine history, i.e. onset, association with menstruation or premenstrual syndrome, course during pregnancy and menopause, will be discussed in order to expand the knowledge of reproductive endocrinology in the management of migraine in women.