Previous research has demonstrated optimized processing of motivationally significant stimuli early in perception. In the present study, the time course and underlying mechanisms for such fast differentiation are of interest. We investigated the involvement of the primary visual cortex in affective evaluation of conditioned stimuli (CSs). In order to elicit learning within the visual system we chose affective pictures as unconditioned stimuli and used laterally presented gratings as CSs. Using high-density electroencephalography, we demonstrated modulation of the C1 visual event-related component for threat-related stimuli versus neutral stimuli, which increased with continuing acquisition of affective meaning. The differentiation between aversive and neutral visual stimuli occurred as early as 65–90 ms after stimulus onset and suggested involvement of the primary visual areas in affective evaluation. As an underlying mechanism, we discuss short-term reorganization in visual cortex, enabling sensory amplification of specific visual features that are related to motivationally relevant information.