For current and future applications of human intestinal organoids (hIOs) to various aspects of in vivo research and their potential clinical use, an efficient noninvasive system is needed to directly visualize the stage of intestinal differentiation and graft-host interactions and for further safety monitoring and efficacy. Here, we describe a detailed method for monitoring and histologically identifying implanted hIO-expressing eGFP and mCherry fluorescence under the kidney capsule of immunodeficient mice with fluorescence imaging (FLI). We then describe the orthotropic transplantation method of hIOs and methods to confirm successful engraftment in the small intestines of immunodeficient mice. These methods provide an approach for tracking the location of intestinal cells in hIOs in vivo and ex vivo using a fluorescent reporter system from the beginning of engraftment to various subsequent experiments.