Natural orifice endoscopy in small animal models has been limited in the past by instrument size and optical performance. In this report, we investigate the feasibility of using a recently developed microvideo endoscopy system to evaluate the colon microcirculation. Using a murine model of acute colitis, microvideo endoscopy was useful in mapping the topography of inflammation as well as identifying relevant structures in the microcirculation. We conclude that natural orifice endoscopy is a useful method for the minimally invasive longitudinal assessment of the colonic mucosal microcirculation.