Trigeminal nerve-mediated pain disorders such as migraine, temporomandibular joint disorder, and classical trigeminal neuralgia are more prevalent in women than in men. Female laboratory animals also show greater responses to various nociceptive stimuli than male animals. However, current knowledge of migraine pathogenesis is based primarily on experimental studies conducted in male animals and lack of migraine research with female animals limits clinical relevance. Migraine is triggered by any alteration in the intrinsic or extrinsic milieu and women at reproductive age are continuously prone to waxing and waning effects of female sex hormones. The experimental approach to this problem is complex because the rodent estrous cycle differs from the human cycle, and because exogenous hormone replacement in ovariectomized females has its limitations. The existence of multiple estrogen receptors in the trigeminal system also presents a challenge. Estrogens do not seem to directly affect calcitonin gene-related peptide or 5-HT1D receptors in the trigeminal system. Nonetheless, 2 estrogen receptors activate MAPK/ERK signaling pathway that mediates nociceptive processing in trigeminal nucleus caudalis. In addition, estrogen enhances susceptibility to cortical spreading depression, the neurobiological event underlying migraine aura, which may be independent of the estrous cycle. Further studies in female animals are required to clarify mechanisms underlying sex differences with respect to fluctuating sex hormones, cortical spreading depression, and excitability of the trigeminovascular system.