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Background To apply effective connectivity by means of nonlinear Granger Causality (GC) and brain networking analysis to basal EEG and under visual stimulation by checkerboard gratings with 0.5 and 2.0 cpd as spatial frequency in migraine with aura (MA) and without aura (MO), and to compare these findings with Blood Oxygen Level Dependent (BOLD) signal changes. Methods Nineteen asymptomatic MA and MO patients and 11 age and sex matched controls (C) were recorded by 65 EEG channels. The same visual stimulation was employed to evaluate BOLD signal changes in a subgroup of MA and MO. The GC and brain networking were applied to EEG signals. Results A different pattern of reduced vs increased GC respectively in MO and MA patients, emerged in resting state. During visual stimulation, both MA and MO showed increased information transfer toward the fronto-central regions, while MA patients showed a segregated cluster of connections in the posterior regions, and an increased bold signal in the visual cortex, more evident at 2 cpd spatial frequency. Conclusions The wealth of information exchange in the parietal-occipital regions indicates a peculiar excitability of the visual cortex, a pivotal condition for the manifestation of typical aura symptoms. Electronic supplementary material The online version of this article (10.1186/s10194-017-0803-5) contains supplementary material, which is available to authorized users.