Traditional cell cultures have long been fundamental to biological research, offering an alternative to animal models burdened by ethical constraints and procedural intricacies, often lacking relevance to human physiology and disease. Moreover, their inability to accurately represent the intricate cellular diversity and functionality observed in living organisms as well as their limited effectiveness in generating tissue-relevant architectures, restricting our understanding of biological and disease mechanisms. Organoid technology established itself as breakthrough addressing these limitations. Leveraging the intricate ability of stem cells to self-renew and differentiate, organoids are cultivated under conditions mimicking their tissue of origin, yielding three-dimensional structures through processes reminiscent of those in vivo. The resulting tissue models exhibit striking similarities to native tissues in terms of genetic expression, cellular functionality, and structural architecture, holding immense promise for biomedical research. Yet, challenges persist in their application, owing to their inherently complex and closed structures, hindering experimental accessibility and long-term studies. This thesis presents the development of a platform tailored for constructing organoid-based models of gastrointestinal epithelia, aimed to overcome the limitations of traditional organoids by offering bilaterally accessible structures with enhanced observability. This thesis demonstrates the generation of murine gastric, small intestinal, caecal, and colonic epithelial models, faithfully recapitulating tissue geometries and exhibiting high physiological relevance, validated by the regionalization of stem and differentiated cells and transcriptional resemblance to native epithelia. The thesis explores also the advantages of air-liquid interface (ALI) cultures in enhancing transcriptional fidelity and cellular motility in gastric tissue models. An important highlight of the patform is demonstrated through infection studies involving the caecal model infected with Trichuris muris larvae, by the description of observations made regarding interactions between the larvae and the host epithelium such as larval invasion and syncytial tunnel formation. Additionally, this thesis presents the development of a human stomach model system with bilateral access, that enabled the simulation of apical acid conditions akin to those found in the actual stomach. Under these physiological conditions, the model could generate mature pit cells, which are absent in traditionally cultivated organoids. Intriguingly, upon infection with the pathogen Helicobacter pylori, these cells exhibit a response distinctive of those of other cell types. These findings underscore the pivotal role of these cells in orchestrating the immune response, and indicate their potential as a target for therapeutic interventions. In summary, the newly developed system provides a flexible platform for in vitro studies of gastrointestinal epithelia, adaptable to diverse research needs. The investigations presented have expanded insights into gastrointestinal stem cell dynamics as well as the organisation and maintenance of the epithelium. Additionally, the pathogen infection experiments highlighte the value of the setups in advancing our comprehension of gastrointestinal disorders and health.