The short-lasting primary headache syndromes may be conveniently divided into those exhibiting marked autonomic activation and those without autonomic activation. The former group comprise chronic and episodic paroxysmal hemicrania, short-lasting unilateral neuralgiform headache with conjunctival injection and tearing (SUNCT syndrome) and cluster headache. These headache syndromes are compared with other short-lasting headache disorders, such as hypnic headache, and persistent headache with milder autonomic features such as hemicrania continua. Cluster headache is included with the shorter-lasting headaches to attempt a nosological analysis of these syndromes. The paroxysmal hemicranias are characterized by frequent short-lasting attacks of unilateral pain usually in the orbital, supraorbital or temporal region that typically last minutes. The attack frequency usually ranges from 5 to 40 attacks per day. The pain is severe and associated with autonomic symptoms such as conjunctival injection, lacrimation, nasal congestion, rhinorrhoea, ptosis or eyelid oedema. Almost all reported cases respond to treatment with indomethacin, but respond poorly to other treatments including other nonsteroidal anti-inflammatory drugs. A recent case study demonstrated the release of both trigeminal and parasympathetic neuropeptides during a bout of pain in the same pattern previously described in cluster headache. The SUNCT syndrome is a distinctive rare condition characterized by less severe pain but marked autonomic activation during attacks. Consistent with previous reports, the present case of SUNCT syndrome was intractable to therapy. The similarites of these syndromes suggests a considerable shared pathophysiology. It is suggested that the syndromes are sufficiently well established for inclusion in the International Headache Society Classification system and that trigeminal-autonomic cephalalgias should be classified as a group together. A proposed re-classification is presented.