Induced pluripotent stem cells (iPSCs) technology provides unique possibilities for human disease modeling and novel therapeutic approach in regenerative medicine. By applying this technology, it is possible to establish high-fidelity human disease models from biopsy samples of different individuals with various genetic backgrounds. This may provide a better understanding of patient-specific pathophysiological processes of a wide variety of diseases. Stem cell-derived intestinal epithelia and human intestinal organoids (HIOs) generated in vitro, for example, can faciliate drug screening and modeling of inflammation-associated gastrointestinal diseases. In this review, we highlight novel achievements of generating disease-related iPSCs and discuss their potential applications in the modeling of gastrointestinal disorders. The critical influencing factors, main limitations and possible improvements in the process of iPSCs-based disease modeling are also discussed.