A side-view dual axes confocal endomicroscope is demonstrated that can be inserted repetitively in hollow organs of genetically engineered mice for in vivo real-time imaging in horizontal and vertical planes. Near infrared (NIR) excitation at λ_ex = 785 nm was used. A monolithic 3-axis parametric resonance scan mirror was fabricated using micro-electro-mechanical systems (MEMS) technology to perform post-objective scanning in the distal end of a 4.19 mm diameter instrument. Torsional and serpentine springs were designed to “switch” the mode of imaging between vertical and horizontal planes by tuning the actuation frequency. This system demonstrated real-time in-vivo images in horizontal and vertical planes with 310 µm depth and 1.75 and 7.5 µm lateral and axial resolution. Individual cells and discrete mucosal structures could be identified.