Primary headaches are known to be associated with multiple sclerosis (MS), but previous studies concerning this relationship are not conclusive. Nowadays, there are no studies assessing the prevalence of headaches in Polish MS patients. The aim of the study was to assess the prevalence and characterise headaches in MS patients treated with disease-modifying therapies (DMTs). In a cross-sectional study of 419 consecutive RRMS patients, primary headaches were diagnosed according to the International Classification of Headache Disorders (ICHD-3) criteria. Primary headaches were observed in 236 (56%) of RRMS patients, with a higher prevalence in women (ratio of 2:1). The most common was migraine 174 (41%) (migraine with aura 80 (45%), migraine without aura 53 (30%), and probable migraine without aura 41 (23%); less frequent was tension-type headache 62 (14%). Female sex was a risk factor for migraines but not for tension-type headaches (p= 0.002). Migraines mostly started before MS onset (p= 0.023). Migraine with aura was associated with older age, longer disease duration (p= 0.028), and lower SDMT (p= 0.002). Longer DMT time was associated with migraine (p= 0.047), particularly migraine with aura (p= 0.035). Typical for migraine with aura were headaches during clinical isolated syndrome (CIS) (p= 0.001) and relapses (p= 0.025). Age and type of CIS, oligoclonal band presence, family MS history, EDSS, 9HTP, T25FW, and type of DMT did not correlate with headache. Headaches are present in more than half of MS patients treated with DMTs; migraines occur almost three times more frequently than tension-type headaches. Migraines with aura headaches during CIS and relapses are typical. Migraine in MS patients had high severity and typical migraine characteristics. DMTs had no correlation with the presence or type of headache.