The temporal dynamics and anatomical correlates underlying human visual cognition are traditionally assessed as a function of stimulus properties and task demands. Any non-stimulus related activity is commonly dismissed as noise and eliminated to extract an evoked signal that is only a small fraction of the magnitude of the measured signal. We review studies that challenge this view by showing that non-stimulus related activity is not mere noise but that it has a well-structured organization which can largely determine the processing of upcoming stimuli. We review recent evidence from human electrophysiology that shows how different aspects of pre-stimulus activity such as pre-stimulus EEG frequency power and phase and pre-stimulus EEG microstates can determine qualitative and quantitative properties of both lower and higher-level visual processing. These studies show that low-level sensory processes depend on the momentary excitability of sensory cortices whereas perceptual processes leading to stimulus awareness depend on momentary pre-stimulus activity in higher-level non-visual brain areas. Also speed and accuracy of stimulus identification have likewise been shown to be modulated by pre-stimulus brain states.