BACKGROUND: Results from transcranial magnetic stimulation (TMS) studies of visual cortex have confirmed visual cortical hyperexcitability in patients with migraine. It has been speculated that this may be due to deficient intracortical inhibitory tone. However, the TMS induction of phosphenes relies on the reporting of a subjective experience, and may thus be subject to bias. METHODS: Seven migraineurs with visual aura and seven sex- and age-matched controls were studied. Fifty-four different three-letter combinations were briefly displayed and followed by a magnetic pulse at 40, 70, 100, 130, 160, and 190 msec. Subjects were required to report as many letters as they thought they had recognized. RESULTS: In the migraine group, the mean proportion of correctly identified letters was significantly higher at 100 msec, as was the proportion of trials with two or three letters correctly reported. The time window in which perceptual suppression could be introduced was narrower in migraineurs compared to controls. CONCLUSION: These findings suggest that inhibitory systems are activated to a lesser extent by TMS pulses in patients. This observation is in agreement with the hypothesized deficiency of intracortical inhibition of the visual cortex, at least in migraineurs with aura.