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Advances in stem cell research in recent decades have been aided by progress in the development of novel technologies aimed at biological systems. At the same time mimicking stem cell niches in vitro has become crucial for both basic stem cell research and the development of innovative therapies based on stem cells. Innovative microscale technologies can contribute to our quantitative understanding of how phenomena at the microscale can determine stem cell behavior based on our increasing ability to control culture conditions and the throughput of data while reducing times and costs. In particular, microtechnologies must be designed and developed to capture the complexity of cell–substrate, cell–cell, and cell–soluble environment interactions considering the characteristic time and length scales of biological phenomena. While acknowledging the advantages of applying these technologies to stem cell culture, this chapter focuses on issues related to the control and mimicking of microenvironmental cues of the stem cell niche, such as substrate properties, cell topology, the soluble environment, and the electrophysiology.