SUNCT (Short-lasting Unilateral Neuralgiform headache attacks with Conjunctival injection and Tearing) and SUNA (Short-lasting Unilateral Neuralgiform headache attacks with cranial Autonomic symptoms) are rare primary headache syndromes, classified as Trigeminal Autonomic Cephalalgias (TACs). Hypothalamic involvement in the TACs has been suggested by functional imaging data and clinically with deep brain stimulation. Fifty-two patients (43 SUNCT, 9 SUNA) were studied to determine the clinical phenotype of these conditions and response to medications. A functional imaging study explored activation of the posterior hypothalamus in attacks of SUNCT/SUNA. The clinical study characterised SUNCT and SUNA in terms of epidemiology, phenotype and clinical characteristics. Indomethacin is ineffective on single-blind testing. Intravenous lidocaine was effective in all cases. Open-label trails showed the effectiveness of lamotrigine, topiramate and gabapentin. On functional imaging there was hypothalamic activation bilaterally in 5/9 SUNCT patients, and contralaterally in two patients. Two SUNCT patients had ipsilateral negative activation. In SUNA the activation was bilaterally negative. There was no hypothalamic activation in a patient with SUNCT secondary to a brainstem lesion. The data suggests that there should be revised classification for SUNCT and SUNA, with an increased range of attack duration and frequency, cutaneous triggering of attacks, and a lack of refractory period. The concept of 'attack load' is introduced. The lack of response to indomethacin and the response to intravenous lidocaine, are useful in diagnostic and therapeutic terms, respectively. Preventive treatments include lamotrigine, gabapentin and topiramate. The role of hypothalamic involvement in SUNCT and SUNA as TACs is considered.