We have reported a preliminary study confirming hyperexicitability of occipital cortex in migraine with aura (MwA) using transcranial magnetic stimulation (TMS). We have now completed a blinded study to investigate the occipital cortex in MwA and without aura (MwoA) compared with normal controls (NC) using TMS. TMS was performed using the Caldwell MES-10 stimulator. A circular coil 9.5 cm diameter was applied to the occipital scalp (7 cm above the inion). Stimulator intensity was increased in 10% increments until subjects reported visual phenomena or 100% intensity was reached. Stimulation intensity was then fine tuned to determine the threshold at which phosphenes were seen. Fisher's exact t-test and logrank test were used for statistical comparisons. Ten subjects with MwA and MwoA were compared to 10 NC. The difference in the proportion of subjects with phosphene generation was statistically significant (MwA 100%, MwoA 60% and NC 30%) [P = 0.003]. The difference in threshold levels for phosphenes was also significant for MwA 42.8%, and controls 57.3% [P = 0.0001]. There is a difference in threshold for excitability of occipital cortex in MwA and MwoA compared to NC. This is a direct neurophysiological correlate for clinical observations, which have inferred hyperexicitability of the occipital cortex in migraineurs.