We used transcranial magnetic stimulation (TMS) with a figure-of-eight coil to excite motor and visual V1-V2 cortices in patients suffering from migraine without (MO) (n = 24) or with aura (MA) (n = 13) and in healthy volunteers (HV) (n = 33). Patients who had a migraine attack within 3 days before or after the recordings were excluded. All females were recorded at mid-cycle. Single TMS pulses over the occipital cortex elicited phosphenes in 64% of HV, 63% of MO and 69% of MA patients. Compared with HV, the phosphene threshold was significantly increased in MO (P = 0.001) and in MA (P = 0.007), but there was no difference between the two groups of migraineurs. The motor threshold tended to be higher in both migraine groups than in HV, but the differences were not significant. In conclusion, this study shows that two-thirds (64.86%) of patients affected by either migraine type present an increased phosphene threshold in the interictal period, which suggests that their visual cortex is hypoexcitable.