Visual-induced alpha desynchronization (VID) and visual-evoked potentials (VEPs) characterize occipital activation in response to visual stimulation but their exact relationship is unclear. Here, we tested the hypothesis that VID and VEPs reflect different aspects of cortical activation. For this purpose, we determined whether VID and VEPs are differentially modulated by low-frequency repetitive transcranial magnetic stimulation (rTMS) over the occipital pole. Scalp EEG responses to visual stimuli (flashed either to the left or to the right visual field) were recorded for 8 min in six healthy subjects (1) before, (2) immediately following, and (3) 20 min after left occipital rTMS (1 Hz, 10 min). The parameters aimed to reduce cortical excitability beyond the end of the TMS train. In addition, simple reaction times to visual stimulation were recorded (left or right hand in separate blocks). In all subjects, VID was significantly and prominently reduced by rTMS (P = 0.0001). In contrast, rTMS failed to modulate early VEP components (P1/N1). A moderate effect was found on a late VEP component close to manual response onset (P = 0.014) but this effect was in the opposite direction to the VID change. All changes were restricted to the targeted left occipital cortex. The effects were present only after right visual field stimulation when a right hand response was required, were associated with a behavioral effect, and had washed out 20 min after rTMS. We conclude that VID and early VEPs represent different aspects of cortical activation. The findings that rTMS did not change early VEPs and selectively affected VID and late VEPs in conditions where the visual input must be transferred intrahemispherically for visuomotor integration (right visual field/right hand) are suggestive of rTMS interference with higher-order visual functions beyond visual input. This is consistent with the idea that alpha desynchronization serves an integrative role through a corticocortical "gating function."