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 highfidelity 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.