The aim was to describe the consulting behaviour and clinical outcomes of children presenting with headache in primary care. This was a historical cohort study using data from the UK General Practitioner Research Database. Cases were children aged 5-17 years who presented to primary care with primary headache (migraine, tension-type headache, cluster headache) or undifferentiated headache (no further descriptor). Controls were age, sex and practice matched. Their records were examined for consultations, referrals, relevant treatments and specific diseases in the subsequent year. Children with headache (n = 48 575) were identified and matched to controls. At presentation, 9321 (19.2%) of headaches were labelled primary, 549 (1.1%) secondary and 38 705 (79.7%) received no formal diagnosis. Of the latter group, 2084 (5.4%) received a primary headache diagnosis in the subsequent year. Following a diagnosis of migraine, 258 (3.5%) had received a triptan and 1598 (21%) were using propranolol or pizotifen. Total consultations were higher in cases than in controls in the year before the headache: cases ages 5-8 years, mean (s.d.) 5.0 (4.0) consultations; controls 4.0 (3.5) consultations. In 1 year controls had 43 430 consultations, of which 256 (0.6%) were for headache, of whom 64 (25%) were referred to secondary care. Headache was a risk factor for benign and malignant tumours, cerebrovascular disease, primary disorders of raised intracranial pressure and depression. This risk was reduced if a diagnosis of a primary headache disorder could be made. Although there is an increased likelihood of a serious pathology with headache presentations, the risk is small particularly if a diagnosis of a primary headache is made. General practitioners are likely to be underdiagnosing migraine. This study can inform management guidelines for new presentations of headache in primary care, particularly when a secondary pathology is suspected.