Currently, no low cost commercial 3D active glasses with embedded eye tracker are available despite the importance of 3D and eye tracking for numerous applications. In this context, a simple low cost eye tracker for 3D glasses with liquid crystal shutters is presented and tested for orthoptics applications. By using a beam splitter to better align the camera with the line of sight when the subject looks at a target in front of him at far range, the new design allows recording high quality images with limited pupil deformation when compared to other commercial eye trackers where the cameras can be far from this axis (head mounted or fixed). Such a design could be useful for various applications from orthoptics to virtual reality