A two-axis scanning catheter was developed for 3D endoscopic imaging with spectral domain optical coherence tomography (SD-OCT). The catheter incorporates a micro-mirror scanner implemented with microelectromechanical systems (MEMS) technology: the micro-mirror is mounted on a two-axis gimbal comprised of folded flexure hinges and is actuated by magnetic field. The scanner can run either statically in both axes or at the resonant frequency (>= 350Hz) for the fast axis. The assembled catheter has an outer diameter of 2.8 mm and a rigid part of 12 mm in length. Its scanning range is +/- 20 in optical angle in both axes with low voltages (1 approximately 3V), resulting in a scannable length of approximately 1 mm at the surface in both axes, even with the small catheter size. The catheter was incorporated with a multi-functional SD-OCT system for 3D endoscopic imaging. Both intensity and polarization-sensitive images could be acquired simultaneously at 18.5K axial scans/s. In vivo 3D images of human fingertips and oral cavity tissue are presented as a demonstration.