Previous studies have suggested complex modes of physiological stapes motions based upon various measurements. The goal of this study was to analyze the detailed errors in measurement of the complex stapes motions using Laser Doppler Vibrometer (LDV) systems, which are highly sensitive to the stimulation intensity and the exact angulations of the stapes. Stapes motions were measured with acoustic stimuli as well as mechanical stimuli using a custom-made three-axis piezoelectric actuator, and errors in the motion components were analyzed. The ratio of error in each motion component was reduced by increasing the magnitude of the stimuli, but the improvement was limited when the motion component was small relative to other components. This problem was solved with an improved reflectivity on the measurement surface. Errors in estimating the position of the stapes also caused errors on the coordinates of the measurement points and the laser beam direction relative to the stapes footplate, thus producing errors in the 3-D motion components. This effect was small when the position error of the stapes footplate did not exceed 5 degrees.