3-D optical coherence tomography (OCT) has been extensively investigated as a potential screening and/or surveillance tool for Barrett's esophagus (BE). Understanding and correcting motion artifact may improve image interpretation. In this work, the motion trace was analyzed to show the physiological origin (respiration and heart beat) of the artifacts. Results showed that increasing balloon pressure did not sufficiently suppress the physiological motion artifact. An automated registration algorithm was designed to correct such artifacts. The performance of the algorithm was evaluated in images of normal porcine esophagus and demonstrated in images of BE in human patients.