When each video sequence is captured, an inappropriate camera motion should be one of crucial factors leading to visual discomfort and distortion. The well known symptom, visually induced motion sickness (VIMS) is caused by the illusion of self motion by perceiving the video with ego motion. In particular, for the stereoscopic 3D video, it can be easily observed that the viewers have dominantly feel much more severe symptoms of visual discomfort. In this paper, we analyze the ego motion of the stereoscopic video and predict the effects. We attempt a novel approach by exploiting the computer vision algorithm. We propose a novel method which can estimate the perceptual 3D ego motion from the stereoscopic video. Then we analyze the ego motion components to predict the visual discomfort of stereoscopic video.