Hematopoietic stem cells (HSCs) reside in the bone marrow (BM) niche in a noncycling state and enter the cell cycle at long intervals. This unique property of HSCs is reminiscent of hibernation in mammals. However, little is known about inter- and intracellular signaling mechanisms underlying this unique property of HSCs. This is largely due to the paucity of HSCs making application of traditional signal transduction assays difficult. To address these issues, we have developed a novel assay based on in-droplet single-cell staining and quantitative fluorescence imaging analysis. Using this assay system, we demonstrate that freshly isolated HSCs from the BM niche lack lipid raft clustering, exhibit repression of the AKT-FOXO signaling pathway, and express abundant p57(Kip2) cyclin-dependent kinase inhibitor. Lipid raft clustering induced by cytokines was essential for HSC re-entry into the cell cycle. Conversely, inhibition of lipid raft clustering caused sustained nuclear accumulation of FOXO transcription factors and induced HSC hibernation ex vivo. Among niche signals examined, transforming growth factor-beta (TGF-beta) efficiently inhibited lipid raft clustering and induced p57(Kip2) expression, leading to HSC hibernation. These data uncover a critical role for lipid rafts in HSC fate decision and establish the role of TGF-beta as a niche signal in control of HSC hibernation in the BM niche.