Migraine is more likely to be misdiagnosed in patients with comorbid diseases. Not only primary care physicians, but also specialists might misdiagnose it due to the lack of diagnostic criteria awareness. The ID migraine test is a reliable screening instrument that may facilitate and accelerate migraine recognition. This study aimed to compare the prevalence and characteristics of migraine in a large sample of patients admitted to clinics of ophthalmology (OC), ear, nose and throat diseases (ENTC) and neurology (NC), as well as to validate the use of the ID migraine test in OC and ENTC settings. This was a multicentre (11 cites) study of out-patients admitting either to NC, ENTC or OC of the study sites during five consecutive working days within 1 week. From each of the clinics, 100 patients were planned to be recruited. All recruited patients were interviewed and those having a headache complaint received an ID migraine test and were examined for headache diagnosis by a neurologist, blinded to the ID migraine test result. A total of 2625 subjects were recruited. Only 1.3% of OC patients and 5.4% of ENTC patients have been admitted with a primary complaint of headache, whereas the percentage of NC patients suffering from headache was 37.6%. Whereas 138 patients (19.3%) in OC, 154 (17.3%) in ENTC and 347 (34%) in NC were found to be ID migraine test positive, 149 patients (20.8%) in OC, 142 (16%) in ENTC and 338 (33.1%) in NC were diagnosed with migraine. The sensitivity, specificity, and positive and negative predictive ratios of the ID migraine test were found to be similar in all clinics. An important fraction of the patients admitted to NC, as well as to OC and ENTC, for headache and/or other complaints were found out to have migraine by means of a simple screening test. This study validated the ID migraine test as a sensitive and specific tool in OC and ENTC, encouraging its use as a screening instrument.