Multiple 5-HT receptor subtypes contribute to a variety of region-specific functional effects. The raphé nuclei control nociceptive inputs by releasing 5-HT in the brainstem, whereas dural mast cells provide the humoral source of 5-HT in the meninges. Triptans (5-HT 1B/D agonists) and ditans (5-HT 1F agonists) are the best established 5-HT anti-migraine agents. However, activation of meningeal afferents via ionotropic 5-HT 3 receptors results in long-lasting excitatory drive suggesting a pro-nociceptive role for these receptors in migraine. Nevertheless, clinical data do not clearly support the applicability of currently available 5-HT 3 antagonists to migraine treatment. The reasons for this might be the presence of 5-HT 3 receptors on inhibitory interneurons dampening the excitatory drive, a lack of 5-HT 3A-E subunit-selective antagonists and gender/age-dependent effects. This review is focusing on the controversial role of 5-HT 3 receptors in migraine pathology and related pharmacological perspectives of 5-HT ligands.