In order to employ pluripotent stem cells in the field of regenerative medicine, it is necessary to establish a large-scale culture system for cell differentiation. We have developed a novel three-dimensional method for culturing human induced pluripotent stem (iPS) cells, using hollow fibers (HFs). The cells immobilized inside HFs can proliferate and form multicellular aggregates, capable of achieving a high cell density and promoting further spontaneous cell differentiation. We first cultured human iPS cells for 7 days under conditions that maintained their undifferentiated state and then switched the culture conditions to allow spontaneous cell differentiation. In the 7-day undifferentiated culture, a high cell density of approximately 10-fold that of the initial seeding density was achieved. The upregulation of gene markers for differentiation such as CXCR4 or SOX17 was observed in the culture of differentiated cells. Expression of the lineage-specific cell-surface marker CXCR4 was about 30% at day 5 in the differentiation culture, which was 2-fold higher than that in the traditional monolayer culture. After HF culture, we obtained the CXCR4-positive cell population and performed monolayer culture for further differentiation of the hepatic lineage. In the CXCR4-positive cell population, the expression levels of a few liver-specific gene markers tended to increase. However, there were no significant differences between the separation and non-separation groups, which indicates the need for refinement of the cell separation process and cell maturation procedure in future studies. In conclusion, the HF culture method has potential for achieving the large-scale culturing and spontaneous differentiation of human iPS cells. (C) 2019, The Society for Biotechnology, Japan. All rights reserved.