Pathophysiological concepts of primary headache diseases have been developed significantly in the last decades. Nevertheless pathophysiology of single diseases is unexplained. Migraine headache arises from activation and sensibilization of trigeminal nociceptors, essential processes are located at the meninges and the meningeal vessels. Calcitonin generelated peptide (CGRP) seems to have essential importance concerning migraine and cluster headache. Mechanisms leading to peripheral and central sensitization are relevant in chronification of migraine and tension-type headache. As a higher-level centre the hypothalamus seems to have an essential meaning in the initiation of migraine attacks. Dysbalance between the sympathetic and parasympathetic neural system causes cranial-autonomic symptoms in some headache diseases and can be affected therapeutically.