The aim of this study was to investigate the association between headache and asthma, bronchodilators and atopy in school children. A cross-sectional survey of all primary school children was conducted in two towns near Newcastle, New South Wales, Australia; one in the vicinity of two coal-fired power stations, the other free of outdoor industrial air pollution. The main outcome measures were frequent headache, wheezing, bronchial reactivity, use of bronchodilators and atopy. Eight hundred and fifty-one primary school children aged 5-12 years participated (92% response rate). Twenty-three per cent of the children were reported to have had a history of frequent headache. Crude odds ratios indicated that the odds of frequent headache was significantly higher in children with asthma and atopy and where there was a smoker in the home, but that there was no association between frequent headache and use of bronchodilators or the sex of the child or socio-economic status measured as father's occupation. Stepwise logistic regression with frequent headache as the outcome of interest showed that, after adjusting for age and smoking in the home, the odds ratio for asthma (defined as current wheeze) was 3.24 (95% confidence interval [CI] 2.19-4.77). The similarly adjusted odds ratio for asthma defined as bronchial hyperreactivity (BHR) was 1.60 (95% CI 1.09-2.37). Atopy was not statistically significantly associated with headache for either model. Asthma (defined as wheeze or BHR) is an independent risk factor for frequent headache. The relationship between headache and asthma is an association with bronchial hyperresponsiveness rather than atopy.