Human induced pluripotent stem cells (hiPSC) have been used to generate intestinal organoids that mimic key intestinal properties without the requirement for invasive procedures to obtain human tissues. The main protocols that have been described result in gut organoids that contain both intestinal epithelium as well as mesenchymal cells (2, 3). We have previously reported on human iPSC-derived intestinal organoids that can be propagated in long-term culture which contain solely epithelial cells (4–6). A pure epithelial model offers unique opportunities to study epithelial cell intrinsic and cell type specific mechanisms. Among these cellular processes are epigenetic mechanisms such as DNA methylation, which acts as a key regulator of intestinal epithelial development and regional identity (1, 7). The purpose of this study was to characterise iPSC-derived human intestinal epithelial organoids (iPSCo) by comparing these cultures with primary purified intestinal epithelial cells (IEC).