BACKGROUND: Visual aura is present in about one-third of migraine patients and triggering by bright or flickering lights is frequently reported. METHOD: Using migraine with visual aura patients, we investigated the neurochemical profile of the visual cortex using magnetic resonance spectroscopy. Specifically, glutamate/creatine and GABA/creatine ratios were quantified in the occipital cortex of female migraine patients. RESULTS: GABA levels in the occipital cortex of migraine patients were lower than that of controls. Glutamate levels in migraine patients, but not controls, correlated with the blood-oxygenation-level-dependent (BOLD) signal in the primary visual cortex during visual stimulation. CONCLUSION: Migraine with visual aura appears to disrupt the excitation-inhibition coupling in the occipital cortex.