We studied disparity-evoked responses in natural scenes using high-density electroencephalography (EEG) in an event-related design. Thirty natural scenes that mainly included outdoor settings with trees and buildings were used. Twenty-four subjects viewed a series of trials composed of sequential two-alternative temporal forced-choice presentation of two different versions (two-dimensional [2D] vs. three-dimensional [3D]) of the same scene interleaved by a scrambled image with the same power spectrum. Scenes were viewed orthostereoscopically at 3 m through a pair of shutter glasses. After each trial, participants indicated with a key press which version of the scene was 3D. Performance on the discrimination was >90%. Participants who were more accurate also tended to respond faster; scenes that were reported more accurately as 3D also led to faster reaction times. We compared visual evoked potentials elicited by scrambled, 2D, and 3D scenes using reliable component analysis to reduce dimensionality. The disparity-evoked response to natural scene stimuli, measured from the difference potential between 2D and 3D scenes, comprised a sustained relative negativity in the dominant response component. The magnitude of the disparity-specific response was correlated with the observer's stereoacuity. Scenes with more homogeneous depth maps also tended to elicit large disparity-specific responses. Finally, the magnitude of the disparity-specific response was correlated with the magnitude of the differential response between scrambled and 2D scenes, suggesting that monocular higher-order scene statistics modulate disparity-specific responses.