An active, hardware-based retinal tracker is integrated with a clinical optical coherence tomography (OCT) system to investigate the effects of stabilization on acquisition of high-resolution retinal sections. The prototype retinal tracker locks onto common fundus features, detects transverse eye motion via changes in feature reflectance, and positions the OCT diagnostic beam to fixed coordinates on the retina with mirrors driven by a feedback control loop. The system is tested in a full clinical protocol on subjects with normal and glaucomatous eyes. Experimental analysis software is developed to coalign and coadd multiple fundus and OCT images and to extract quantitative information on the location of structures in the images. Tracking is highly accurate and reproducible on all but one subject, resulting in the ability to scan the same retinal location continually over long periods of time. The results show qualitative improvement in 97% of coadded OCT scans and a reduction in the variance of the position of the optic disc cup edge to less than 1 pixel (<60 μm). The tracking system can be easily configured for use in research on ultra-high-resolution OCT systems for advanced image modalities. For example, tracking will enable very high density 3-D scans of the retina, which are susceptible to eye motion artifacts even for new high-speed systems. © 2005 Society of Photo-Optical Instrumentation Engineers.