We investigated the 1-year prevalence, clinical features and mode of treatment of headache in medical students of the University of Lagos, Nigeria, using a self-administered headache questionnaire. Headache prevalence was 46.0% and was significantly higher in women than in men (62.8% vs. 34.1%). Prevalence of tension-type headache was higher than that of migraine (18.1% vs. 6.4%). Although tension-type headache had a similar prevalence in both sexes (male 17.3%, female 19.2%), migraine was three times more common in women (10.9% vs. 3.2%). A family history of headache was present in 22.0%. Only 4.6% sought medical assistance, whereas 68.2% took non-prescription drugs, mainly simple analgesics. Specific drugs for migraine and tension-type headache were rarely used. In conclusion, 1-year headache prevalence is high among medical students at this university. The low consultation rate and the rarity of usage of specific anti-headache drugs probably reflect inadequacies in the management of primary headaches in this population.