Using pluripotent stem cells, it is now becoming possible to develop tissue models of organ systems within the body. These organs will allow for the study of organ function, physiology, embryology, and even pathologic processes. Recently, our group developed a model of human small intestine developed from human pluripotent stem cells which when transplanted in vivo, produce a mature, cystic intestinal structure that has digestive functions similar to that of native small intestine (Watson et al., 2014). Intestinal permeability is a primordial function of both the epithelium and associated tight junctions to control nutrient intake and prevent the passage of pathogens. One way to study gastrointestinal paracellular permeability is by determining the ability of fluorophores-conjugated macromolecules (i.e., fluorescein isothiocyanate-dextran (FITC-dextran; or FD4) to cross from the lumen and into circulation (Dong et al., 2014). We were able to test the intestinal permeability by injecting FITC-dextran directly into the lumen of the bioengineered intestine and determining the fluorescence within the blood of the murine host at various time points after injection.