Background: Motion detection thresholds with a stationary frame of reference are significantly lower than unreferenced motion thresholds. To account for this, previous studies have postulated the existence of compensatory mechanisms, driven by the presence of a surround, that cancel the effects of eye movements. In the present study we used an adaptive optics scanning laser ophthalmoscope (AOSLO) to investigate the effects of retinal jitter due to fixation eye movements on referenced and unreferenced motion thresholds. Methods: The stimuli were produced by modulation of the AOSLO imaging beam, so that the absolute retinal position of targets was recorded. In Experiment 1 subjects made up/down motion judgments of a dark horizontal bar presented against a stationary 1-degree bright background. In Experiment 2 unreferenced motion thresholds were measured with isolated bright horizontal bars in otherwise complete darkness. In both experiments, AOSLO images for each trial were analyzed offline to extract retinal jitter and the retinal position of targets. Results: For referenced motion, the results were consistent with complete compensation for eye movements by the visual system. In the unreferenced motion case eye movements adversely affected motion judgments, although there was evidence of partial compensation for such eye movements. Conclusions: Compensatory processes completely cancel the effect of fixation jitter for referenced motion but such compensation is partial for unreferenced motion.