BACKGROUND Limited data about the importance of cranial autonomic features of migraines and migrainous features of cluster headaches are available. METHODS We enrolled 2955 patients with migraine and 93 patients with cluster headache. We explored the autonomic features, including ptosis, lacrimation, rhinorrhea, facial swelling, conjunctival injection, and pupil changes. The presence of migrainous features, such as nausea, vomiting, photophobia, and phonophobia, in cluster headache patients were noted. RESULTS Migraine patients with underlying autonomic symptoms (MwuAS) and those without differed significantly. Unilaterality, periocular localization of headaches provoked by starvation, and history of abdominal pain significantly increased the risk of MwuAS. The parameters with the highest sensitivity (94.38%) and specificity (99.89%) for the diagnosis of MwuAS were lacrimation, facial swelling, and conjunctival injection. CONCLUSIONS Migraine and cluster headache are considered two different entities with different pathophysiologies. The assessment of autonomic symptoms is essential, and specialists must consider such an overlap in clinical practice in order to obtain accurate prevalence rates. In particular, lacrimation, conjunctival injection, and facial swelling are widely experienced by migraineurs.