Objectives - Pro-inflammatory mediators are thought to play both peripheral and central roles in migraine pathophysiology. Prostaglandins and leukotrienes, known as the eicosanoids, are degradation products of arachidonic acid and constitute signalization components of inflammatory pathways. This study was designed to assess concentrations of leukotriene E4 (LT-E4) and prostaglandin F2a (PG-F2a) in children with migraine. Materials and Methods This study involved patients aged <= 18 years who presented to the Ondokuz Mayis University Children's Hospital with migrainous headache between January and October 2011. Urinary LT-E4 and PG-F2a concentrations were measured in patients during a headache episode and at a headache-free time and in a control group. Results The patient group consisted of 38 girls and 26 boys aged 5-18 years diagnosed with migraine and having at least 6 months of headache, whereas the control group consisted of 21 girls and 29 boys. Mean +/- standard deviation (SD) urinary LT-E4 concentrations were significantly higher in patients during a migraine episode than in controls (1466.8 +/- 1052.5 pg/ml vs 811.6 +/- 460.0 pg/ml, P < 0.001). In patients with migraine, both urinary LT-E4 (P < 0.001) and PGF-2a (P = 0.021) levels were significantly higher during headache than during non-headache periods. Conclusion - Urinary LT-E4 and PG-F2a were both significantly higher in children with migraine during headache than during non-headache periods. The elevation in the levels of these inflammatory mediators was compatible with the hypothesis relating neuroinflammation in trigeminal vascular blood vessels with migraine pathophysiology. Leukotriene antagonists may be effective in the prophylaxis of migraine attacks.