The small intestine is an important organ in the absorption of orally administrated drugs due to the presence of drug transporters and drug metabolizing enzymes. In preclinical studies, cynomolgus monkey (CM) is frequently used to predict human pharmacokinetics of drugs in small intestine because of its evolutionary closeness to human. However, because there are species differences in small intestinal pharmacokinetics, it is not always possible to predict the in vivo pharmacokinetics in human. By comparing between human and CM, and evaluating species differences, it is expected to lead to accurate prediction of human intestinal pharmacokinetics. Intestinal organoids that mimic the intestinal tissue have attracted attention to drug development. However, the generated organoids are immature, and there is also few report about pharmacokinetics with the intestinal organoids. Therefore, we generated intestinal organoids from human and CM induced pluripotent stem (iPS) cells and analyzed pharmacokinetic functions in this study. Human and CM iPS cells were induced into the hindgut and then were seeded on patterning plates to form uniform spheroids. The floating spheroids were differentiated into intestinal organoids in the medium containing small molecule compounds. In intestinal organoids, the mRNA expression of intestinal markers and pharmacokinetic-related genes was markedly increased by the small molecule compounds. The intestinal organoids had polarized epithelium, and contained various cells constituting small intestinal tissues, which are enterocytes, goblet cells, Paneth cells, enteroendocrine cells, fibroblasts, and smooth muscle cells. The intestinal organoids expressed proteins of a tight junction marker and drug transporters. When the intestinal organoids were incubated with fluorescein isothiocyanate-dextran 4000 (FD-4), accumulation of FD-4 into the organoids was not observed. The efflux of rhodamine123 into the human iPS cell-derived intestinal organoids was observed and inhibited by verapamil, a specific inhibitor of ABCB1/MDR1. In addition, CYP3A activity was detected and inhibited by the specific inhibitor ketoconazole in CM iPS cell-derived intestinal organoids. The mRNA expression and activity of CYP3A were also induced by rifampicin or 1α,25-dihydroxyvitamin D3. In conclusion, we have succeeded in efficiently generating of intestinal organoids with pharmacokinetic functions from human and CM iPS cells using small molecule compounds. Thus, the intestinal organoids would be useful for the prediction of human intestinal pharmacokinetics.