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We present a three-dimensional (3-D) optical coherence tomography (OCT) system based on a dual axis microelectromechanical system (MEMS) mirror. The MEMS mirror provides high-speed, high resolution 2-axis scanning while occupying a very small volume with extremely low power consumption. The dimensions of the mirror are 600×600 μm, and both axes are capable of scanning up to 30 degree angles at frequencies greater than 3 kHz with good linearity. A 3-D image set is acquired when the MEMS mirror is integrated with the fiber-based OCT system. Via 2-axis lateral scanning, combined with an axial scan, a volume (2×2×1.4 mm) image of tissue, including a cancerous region, from a hamster cheek pouch was obtained. Using a signal processing technique, image data is normally presented by 3-volume showing views at arbitrary angles and locations. The objective of this work is to show the capabilities of a 3-D OCT system utilizing a MEMS scanner as this technology can readily by applied to realize OCT beam delivery systems such as hand held scanners and endoscopic probes. A MEMS based 3-D OCT system employing a high speed, small volume scanner may have the potential to expand the application area of OCT and revolutionize areas of clinical medicine as well as medical research.