Objective To examine the association between obesity, medication overuse and chronic daily headaches (CDH) in children, and the relation to headache type and disability. Methods The authors retrospectively evaluated 108 children with chronic daily headaches from their Pediatric Neurology Clinic. Data regarding age, gender, headache type, duration, disability and use of medication, along with height and weight were collected. Body mass index (BMI) was calculated, and percentiles were determined for age and sex. Headache type, disability and use of medications were compared between normal weight, at risk for overweight and overweight children. Results A higher prevalence (39. %) of obesity was found in the whole study group compared to the general population. The diagnosis of transformed migraine, but not of chronic tension type headache, was significantly associated with being at risk for overweight (OR=2.39, 95% CI: 1.2–4.69, P=0.01) or overweight (OR=2.3, 95% CI: 1.3–5.61, P=0.04). Regardless of headache type, a high BMI percentile was associated with increased headache disability and overuse of medications, but not with duration of attacks. Conclusion Obesity and CDH in children are associated. Although obesity seems to be a risk factor for transformed migraine more than for chronic tension type headache, it is associated with increased headache disability and medication overuse regardless of headache type.