Inflammatory bowel diseases (IBD) are characterized by chronic inflammations of the gastrointestinal tract during which the intestinal mucosal barrier gets damaged.Until today, mice models have been used to unravel the complex interactions involved in IBD, yet they often fail to predict human responses. In recent years, organoids have emerged as a game-changer for disease modeling and drug screening. These organoids are three-dimensional (3D) miniaturized versions of an organ that mimic some of the key features of the native tissue in vitro. Traditional organoid culture methods consist of embedding these 3D structures in solidified extracellular matrix (ECM), thus introducing an intrinsic lack of reproducibility and creating highly heterogeneous organoid populations. To overcome these challenges, we use the innovative technology, Gri3D®, a ready-to-use platform for high-throughput and reproducible 3D cultures. Combined with the ImageXpress® Micro Confocal High-Content Imaging System, organoids are monitored at a single-organoid level. We report the induction of an IBD-like phenotype on healthy human rectal organoids using pro-inflammatory cytokines and demonstrate the use of Gri3D as a robust and high-throughput in vitro platform for organoid-based disease modeling.