We propose a new technique to measure the 3D motion of marker points along a straight path within an object using x-ray stereo projections. From recordings of two x-ray projections at different angles, the 3D coordinates of marker points can be determined. By synchronizing the x-ray exposure time to the motion event, a moving marker leaves a trace in the image of which the gray scale is linearly proportional to the marker velocity. By measuring the marker gray scale along the motion path, the velocity at each point is determined and the position as a function of time is obtained by integration. In combination with the 3D information from two stereo recordings, the full 3D motion is obtained. The difference in position between the new method and laser vibrometry was less than 5 mu m. The 3D motion measurement is performed within seconds, making the method ideal for applications in biomechanics. In combination with a full CT-scan of the object, the motion information on the marker points can be used to measure and visualize how an internal rigid 3D structure moves. We demonstrate the method on the malleus ossicle motion in the gerbil middle ear as a function of pressure on the eardrum.