Although therapeutics in Crohn’s disease (CD) have dramatically improved, current approaches targeting the immune system have limited success at a population level. Thus, there is a need for future therapeutics to target different pathways/cell types. Recently, patient derived stem cells have shown promise in helping to better understand the molecular basis of disease. We used patient derived organoids (PDOs), produced from both CD and healthy patients’ pinch biopsies, to determine the ability of PDOs to functionally represent the human intestinal epithelium, and to better understand the role of the epithelium in CD.