Since cognitive and behavioural characteristics of paediatric migraineurs have yet to be adequately defined, in this study we assessed the effect of migraine on the interictal functioning of children and adolescents by comparing the performance of two patient groups, 17 migraineurs with aura (MA) and 31 without aura (MoA) and by correlating the duration of the disorder, the frequency of attacks and interictal period with neuropsychological and behavioural findings. Both patient groups had cognitive performance within normal range except for a significant delay in the reaction time (RT) task. Both MA and MoA revealed a behavioural phenotype characterized by internalizing problems on Child Behaviour Check List (CBCL) scales. Slower RT to simple visual stimuli may be an early sign of a subclinical neuropsychological dysfunction, significantly correlated with the frequency of headache attacks and interictal period. The lack of a control group and other methodological limitations, such as patient selection bias and unadjusted P-value for multiple testing, make it difficult to give this finding a clearcut meaning. Further studies are needed on larger samples compared with a control group.