This paper present a new method to resolve the problem of the estimation of eye position in the analysis of videonystagmography(VNG) sequences, that studies eye vibration using active contour model. An algorithm for horizontal and vertical nystagmus tracking based on some parameters such as position, amplitude and duration, is presented. Indeed, the algorithm uses active contour method to segment the pupil. Thus, segmentation is obtained from Otsu's thresholding, to detect an ellipse region approximates the pupil form. Then, the snake-model uses the estimated ellipse as the initial contour. This proposed approach is approved on clinical samples of the videonystagmography (VNG) from patient who presented a congenital nystagmus.