Organoids, derived from stem cells, are 3D cellular structures that provide a valuable tool for studying immune cell interactions with epithelial cells in health and disease. They overcome limitations of traditional models by preserving the genetic and epigenetic background of their donors and enabling the study of complex microenvironments. Organoids can be used to model diseases such as cancer, inflammatory bowel disease, and tissue regeneration, and when combined with organ-on-chip systems and microfluidics, they allow for precise manipulation and readouts. Genome editing techniques and patient-derived organoids enhance disease modeling and precision medicine. These systems require novel infrastructures like organoid biobanks and drug screening platforms to maximize their impact. Organoids can be co-cultured with immune cells to study interactions, but challenges remain in medium compatibility and cell isolation. Microfluidic systems improve the accuracy of these models by replicating physiological conditions. Organoids are also useful for studying immune-epithelial interactions, tissue regeneration, and microbial co-cultures. They enable the study of genetic variations and mutations, and their use in personalized medicine is growing. Organoid facilities and biobanks are essential for sharing resources and advancing research. High-throughput drug screening and microbial co-cultures are promising applications. Overall, organoids offer a powerful platform for immunological research and disease modeling, with potential for personalized therapies and improved drug development.Organoids, derived from stem cells, are 3D cellular structures that provide a valuable tool for studying immune cell interactions with epithelial cells in health and disease. They overcome limitations of traditional models by preserving the genetic and epigenetic background of their donors and enabling the study of complex microenvironments. Organoids can be used to model diseases such as cancer, inflammatory bowel disease, and tissue regeneration, and when combined with organ-on-chip systems and microfluidics, they allow for precise manipulation and readouts. Genome editing techniques and patient-derived organoids enhance disease modeling and precision medicine. These systems require novel infrastructures like organoid biobanks and drug screening platforms to maximize their impact. Organoids can be co-cultured with immune cells to study interactions, but challenges remain in medium compatibility and cell isolation. Microfluidic systems improve the accuracy of these models by replicating physiological conditions. Organoids are also useful for studying immune-epithelial interactions, tissue regeneration, and microbial co-cultures. They enable the study of genetic variations and mutations, and their use in personalized medicine is growing. Organoid facilities and biobanks are essential for sharing resources and advancing research. High-throughput drug screening and microbial co-cultures are promising applications. Overall, organoids offer a powerful platform for immunological research and disease modeling, with potential for personalized therapies and improved drug development.