Researches for stem cells have been focused on scientists in biomedical sciences as well as clinical application for its great therapeutic potentials. Stem cells have two distinct characteristics: self-renewal and differentiation. In this short review, the links between stem cell research and biomedical engineering is discussed based on the basic characteristics of stem cells. This concept can be extended to the fundamental questions of biological sciences for cells such as proliferation, apoptosis, differentiation, and migration. For understanding proliferation and apoptosis of stem cells, techniques from biomedical engineering such as surface patterning, MEMS, nanotechnologies have been used. The advanced technologies such as microfluidic technologies, three dimensional scaffold fabrication, and mechanical/electrical stimulation have also been used in cell differentiation and migration. Basic and unsolved questions in the stem cell research field have limitations by studying conventional technologies. Therefore, the strategic fusion between stem cell biology and novel biomedical engineering field will break the barriers for understanding fundamental questions of stem cells, which can open the window for the clinical applications of stem cell based therapeutics as well as regeneration of damaged tissues.