The aim of this study was to assess the efficacy of pharmacological prophylactic treatments of migraine in children. Databases were searched from inception to June 2004 and references were checked. We selected controlled trials on the effects of pharmacological prophylactic treatments in children with migraine. We assessed trial quality using the Delphi list and extracted data. Analyses were carried out according to type of intervention. A total of 20 trials were included. Headache improvement was significantly higher for flunarizine compared with placebo (relative risk 4.00, 95% confidence interval 1.60, 9.97). There is conflicting evidence for the use of propranolol. Nimodipine, clonidine, L-5HTP, trazodone and papaverine showed no effect when compared with placebo. All medications were well tolerated and adverse events showed no significant differences. Flunarizine may be effective as prophylactic treatment for migraine in children. Because of the small number of studies and the methodological shortcomings, conclusions regarding effectiveness have to be drawn with caution.