Emotional experience changes visual perception, leading to the prioritization of sensory information associated with threats and opportunities. These emotional biases have been extensively studied by basic and clinical scientists, but their underlying mechanism is not known. The present study combined measures of brain-electric activity and autonomic physiology to establish how threat biases emerge in human observers. Participants viewed stimuli designed to differentially challenge known properties of different neuronal populations along the visual pathway: location, eye, and orientation specificity. Biases were induced using aversive conditioning with only 1 combination of eye, orientation, and location predicting a noxious loud noise and replicated in a separate group of participants. Selective heart rate–orienting responses for the conditioned threat stimulus indicated bias formation. Retinotopic visual brain responses were persistently and selectively enhanced after massive aversive learning for only the threat stimulus and dissipated after extinction training. These changes were location-, eye-, and orientation-specific, supporting the hypothesis that short-term plasticity in primary visual neurons mediates the formation of perceptual biases to threat.