This study investigated whether the individual difference in the observer’s interpupillary distance (IPD) could cause the individual difference in perceived depth in binocular stereopsis. The horizontal retinal disparity (HRD) is one of the most potent depth cues, but the visual system could not uniquely estimate the metric depth from HRD alone. This is because the size of HRD is determined as a function not only of the size of external depth but also of the viewing distance and IPD. Thus to perceive depth veridically from HRD, observers need to adjust the scaling gain (i.e. the magnification factor when converting HRD to perceived depth), taking their IPD into account. To investigate whether the visual system performs such gain calibration, we examined the relationship between IPD size and perceived depth when observing stereograms (i.e. the visual stimulus of fixed HRD) at a fixed viewing distance with 54 observers. The results showed a significant correlation between perceived depth and IPD. This is consistent with the prediction based on the geometric relationship between depth, HRD, IPD, and viewing distance, suggesting that the visual system does calibrate the scaling gain based on the observer’s IPD. However, the measured results did not fully agree with the predictions from the geometry. The results were discussed, focusing on the errors in the estimation of scaling distance.