Endomicroscopy is a technique for obtaining real-time images in vivo, eliminating the need to biopsy a tissue sample. A simple fluorescence endomicroscope can be constructed using a fiber bundle, camera, LED and filters, and individual images can be mosaicked as the probe is moved across the tissue to increase the image size. However, to improve image contrast optical sectioning is required for the removal of returning out-of-focus light. Commonly, this is done using the confocal technique, requiring more expensive laser sources and mechanical scanning mirrors which limits the frame rate. Structured illumination microscopy (SIM) instead uses line patterns projected onto the sample to allow for computational optical sectioning. This eliminates the need for point scanning and allows an incoherent light source, such as an LED, to be used, at the cost of some loss of signal-to-noise ratio. However, as SIM requires multiple images to be combined, motion of the probe results in severe image artefacts, preventing the use of mosaicking techniques. We report a SIM endomicroscope using a digital micro-mirror device (DMD) to generate line patterns at high speed, and with the ability to change the patterns on the fly. Combined with a high-speed camera, this reduces motion artefacts significantly, but not sufficiently to allow for video mosaicking techniques. We therefore demonstrate further reduction of artefacts by orienting the illumination patterns parallel to the direction of motion and performing inter-frame registration and correction. This offers potential for low cost, versatile, optically-sectioned endomicroscopy.