Disruption of the intestinal epithelial barrier is a hallmark of inflammatory bowel disease (IBD). The 3-dimensional colonoid culture system is a useful in vitro model to study intestinal stem cell dynamics and epithelial cell physiology in IBD pathogenesis. However, we have shown that in vivo epithelial changes are not necessarily retained in colonoids established from mice undergoing acute inflammation using a DSS model and primarily reflect stem cell physiology rather than that of terminally differentiated cells.