BACKGROUND Cranial autonomic symptoms (CAS) are distinguishing features of trigeminal autonomic cephalalgias, of which cluster headache (CH) is the most common, but they can occur in patients with migraine. For migraine with strictly unilateral headache, the presence of CAS might cause diagnostic confusion with CH. Characteristics of CAS in migraine and comparisons with those in CH have rarely been reported. METHODS This study prospectively recruited consecutive patients with migraine and CH treated at a headache clinic. Six CAS items were surveyed, including: conjunctival injection, lacrimation, nasal congestion, rhinorrhoea, eyelid oedema and forehead/facial sweating. The CAS characteristics recorded included: laterality, intensity, time sequence and consistency with headache attacks. RESULTS A total of 786 migraine patients (625 women/161 men, mean age 40 (13) years) and 98 CH patients (11 women/87 men, mean age 36 (11) years) were recruited. The prevalence of > or =1 CAS in migraine patients was 56% and did not differ among migraine subtypes. Except for forehead/facial sweating, the features of the other CAS differed between patients with migraine and CH: CAS in migraine tended to be bilateral (OR 5.8-23.8 among different CAS), be unrestricted to the headache sides (OR 5.0-20.4), appear with mild to moderate intensity (OR 1.7-7.7) and be inconsistent with headache attacks (OR 2.8-6.7). CONCLUSIONS CAS were present in half of our migraine patients and the clinical features may help differentiate migraine from CH.