Human pluripotent stem cells (hPSCs) have become a powerful tool to generate the various kinds of cell types comprising the human body. Recently, organoid technology has emerged as a platform to generate a physiologically relevant tissue-like structure from PSCs. Compared to an actual human organ, this structure more closely represents a three-dimensional microenvironment than the conventional monolayer culture system for transplantation, disease modeling, and drug development. Despite its advantages, however, the organoid culture system still has various problems related to culture methods, which have become a challenge for attempts to obtain similar physiological properties to their original tissue counterparts. Here, we discuss the current development of organoid culture methods, including the problems that may arise from the currently available culture systems, as well as a possible approach for overcoming their current limitations and improving their optimum utilization for translational application purposes.