Recent data have suggested that interferon-b (IFN-β) may aggravate headaches in multiple sclerosis (MS) patients. The aim of this study was to investigate the life-time prevalence of primary headaches in MS patients treated with interferons in comparison with patients treated with other disease-modifying agents. Attention was focused on the onset of headache and the changes in pre-existing headaches in relation to the onset of therapy. The study was open-labelled and not randomized. We studied 150 consecutive MS patients treated with IFN-β (109 patients: 54 with 1b, 55 with 1a) and with other drugs (41 patients: 14 with glatiramer acetate, 27 with azathioprine). All patients underwent a semi-structured interview to diagnose headache type, according to the International Headache Society criteria. The frequency of primary headaches was higher in the interferon-group (72%) compared to patients in the other group (54%) (P = 0.03). Worsening of pre-existing headaches or development of de novo headache occurred only in the interferon-group (41 and 48%, respectively) and not in the other group (P<0.001). These results show that headache should be considered among the side-effects of interferon in MS patients.