The diagnosis of Not Otherwise Specified (NOS) headaches in the Emergency Department (ED) is frequent despite many specialist visits performed. The aim of the study was to examine specialist visits carried out in the patients discharged from ED with diagnosis of NOS headache to evaluate discrepancies between specialist and ED diagnosis at discharge. We retrospectively (1.6.2018–31.12.2018) analyzed all the patients admitted with non-traumatic headache to the ED of the tertiary-care University Hospital of Trieste. We evaluated the patients discharged from ED with a final diagnosis of NOS headache and who underwent at least one specialist examination. Demographic data, specialist and ED diagnosis were analyzed. One hundred twenty-four patients (93 F, 31 M, mean age 44 ± 15 years) were included. 71.8% of patients were examined only by a neurologist, 12.9% by non-neurologists, 15.3% by both neurologist and non-neurologist. Only 37% of the patients received a precise diagnosis. Neurologist made a diagnosis slightly more frequently than the other consultants (40.5% vs 37.5%). Neurologists diagnosed primary headaches, headaches secondary to neurological diseases, and facial neuralgia, instead non-neurologists diagnosed only headaches secondary to non-neurological diseases. Primary headaches were diagnosed in 25.7% of cases, migraine being the most frequent. Physicians did not report any specialist diagnoses in the ED discharge sheet. Specialist consultants made specific diagnoses in about one-third of patients that were not reported as final in the discharge records by the ED physician. This leads to a loss of diagnoses and to an overestimation of NOS headache.