The aim was to investigate neuromuscular transmission (NMT) by single-fibre EMG (SFEMG) in a large series of patients having migraine with aura (MA) or cluster headache (CH). Recent studies using SFEMG have shown subclinical dysfunction of NMT in MA and CH. Forty-three patients having MA, 51 with CH and 38 healthy control subjects underwent nerve conduction studies, EMG and SFEMG during voluntary contraction of the extensor digitorum communis muscle. Twenty different potential pairs were recorded and individual, mean and total abnormal individual jitter values were calculated. The results obtained from MA patients were compared with those from CH patients. In MA patients, 32 of 860 jitters were abnormally high, whereas 73 of 1020 of the jitters showed this abnormality in CH patients. None of the control subjects, five MA patients (11.6%) and 11 CH patients (21.6%) were designated as having subclinical NMT abnormality. Thus, patients having junction dysfunction were significantly more common in the CH group. The subclinical NMT abnormality shown by SFEMG is more common in CH than in MA. These two primary headache syndromes may have some shared functional abnormality of NMT constituents which is more evident in CH.