The aim of this study was to characterize the temporal course of phosphene thresholds (PT) using transcranial magnetic stimulation (TMS) in control subjects and in subjects with migraine and to observe whether changes in PT over time can predict a subsequent migraine attack. PTs were measured in 16 migraineurs [nine with aura (MA) and seven without aura (MoA)] and nine controls five times over an approximately 10-week period. Mean PTs were not significantly different between migraineurs and controls; however, there was a trend in MA showing lower thresholds. The minimum threshold values were also smaller in MA subjects than in MoA or control subjects. Generally, PTs had higher variance in migraineurs than in controls, revealing a significant increase in standard deviation of PTs in MA subjects. There was no significant difference of thresholds from the first to the last stimulation in controls and in MoA subjects, but the 3rd, 4th and 5th measurements of MA subjects were significantly lower than their first measurements. Four migraineurs experienced headache within 1 day after one of the measurements. They had either very low or very high PTs compared with the PT values which were not followed by a migraine attack. Our results imply that migraineurs show a higher variability among PT measurements over time than controls, revealing unstable excitability levels in these patients. Additionally, both particularly high and low PTs might predict a subsequent headache in some individuals.