Headache is a common presenting complaint in the Emergency Department. The aim of this study was to delineate the demographic profile of patients presenting a chief complaint of headache and to assess the application of diagnostic algorithms for the management of these patients. We examined patients admitted to the Spedali Civili Hospital ED between January 2005 and December 2009 who complained of headache not related to trauma and all patients hospitalized for headache in Neurological Clinic, from ED, between January 2008 and December 2009. 7495 patients were examined at ED for headaches. 72 % of patients were discharged, 22 % were admitted. From 2005 to 2009, there was a definite decrease in the rate of hospitalization due to headache (15 vs 9.9 % in Department of Neurology and 26 vs 18.9 % in all Departments). Considering the decrease year by year, this reduction was significant from 2007 to 2008, when the algorithms were adopted. The most common diagnosis in the ED was "Non-specific headache" (41 %), followed by "Primary headaches and complications of primary headaches" (20.8 %), "Secondary headaches not associated with risk of serious disease" (20.4 %) and "Secondary headache associated with risk of serious disease" (5 %). Over 2-year period (2008-2009) we found an increase in the diagnosis of "Primary headaches and complications of primary headaches" and "Secondary headaches associated with risk of serious disease" compared with a decrease of "nonspecific headache" and "secondary headaches not associated with risk of serious disease". The use of the diagnostic algorithms and collaborative network between the ED and the Headache Center can improve the management of patients with headache in ED.