This study investigates the effects of stereo disparity on the perception of three-dimensional (3D) object shape. We tested the hypothesis that stereo input modulates the brain activity related to perceptual analyses of 3D shape configuration during image classification. High-density (256-channel) EEG was used to record the temporal dynamics of visual shape processing under conditions of two-dimensional (2D) and three-dimensional (3D) visual presentation. On each trial, observers made image classification judgements (‘Same’/’Different’) to two briefly presented, multi-part, novel objects. On different-object trials, stimuli could either share volumetric parts but not the global 3D shape configuration, have different parts but the same global 3D shape configuration, or differ on both aspects. Analyses using mass univariate contrasts showed that the earliest sensitivity to 2D versus 3D viewing appeared as a negative deflection over posterior locations on the N1 component between 160ms-220ms post stimulus onset. Subsequently, ERP modulations during the N2 time window between 240ms-370ms were linked to image classification. N2 activity reflected two distinct components – an early N2 (240ms-290ms) and a late N2 (290ms-370ms) that showed different patterns of responses to 2D and 3D input, and differential sensitivity to 3D object structure. The results revealed that stereo input modulates the neural correlates of 3D object shape. We suggest that this reflects differential perceptual processing of object shape under conditions of stereo or mono input. These findings challenge current theories that attribute no functional role for stereo input during 3D shape perception.