Numerous research efforts have been directed toward determining the origin of anisotropies of visual space, in contrast to real space. Recent neurophysiological studies have placed the origin in the primary visual cortex (V1) or beyond. The present study sought to provide new psychophysical evidence of the origin of these anisotropies using auto-stereograms as visual stimuli in a relative depth judgment task. The observers were presented with a hidden three-dimensional shape that consisted of two pairs of parallel line segments that were located in different depth planes and oriented at 0° (horizontal line segments), 45°, and 90° (vertical line segments). The influence of orientation on the visual performance of five observers was evaluated. The encountered differences at 45° compared with cardinal orientations revealed a non-conclusive trend toward a negative impact of oblique orientation on the observers' performance. Significant differences were found in accuracy between the horizontal and vertical orientations, and the best scores corresponded to vertical line segments. This finding may be interpreted as the expression of vertical-horizontal anisotropy in depth. The perception of hidden three-dimensional shapes in auto-stereograms occurs beyond the primary visual cortex in the dorsal stream, and the present findings provide psychophysical evidence of the location of vertical-horizontal anisotropy in non-retinotopic areas beyond V1.