Cultivation of stem cells, like all cells in culture, is performed under conditions that cannot and do not replicate normal physiologic conditions. For example, direct exposure of cultured monolayer cells to serum contents is normally prevented in vivo by the vasculature. The heterogeneity of cells and signals between different cell types in an organ is certainly not captured when a single cell type is grown and studied in vitro. Gases, in particular, are not accounted for in routine tissue culture. Oxygen is fundamental for life and its concentration is an important signal for virtually all cellular processes. Nonetheless, oxygen is rarely taken into account in culturing stem and other cells. This review will summarize work that highlights the importance of considering oxygen conditions for culturing and manipulating stem cells. Emphasis is placed on major phenotypic changes in response to oxygen, recognizing that oxygen-mediated transcriptional and post-translational effects are enormously complex, and beyond the scope of this review. The review emphasizes that oxygen is an important signal in all major aspects of stem cell biology including proliferation and tumorigenesis, cell death and differentiation, self-renewal, and migration.