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Manipulation of stem cells is one of the highest goals within biological sciences for the development of devices for the regeneration of injured tissues. In general, the mechanical properties of cells are nowadays recognized to play a role in many cellular phenotypes, including mobility though tissues, survival to mechanical loading and differentiation. Here we present a study where the mechanics of bone marrow CD34+ hematopoietic stem cells (CD34+ cells) and bone marrow stromal cells (BMSCs) is investigated through micropipette aspiration. The objective was to address the role of the nucleus as a central mechanoactive structure in stem cells. Stem cell nuclei occupy most of the cell volume and present different properties from what is known for somatic cells. Mechanics revealed to be highly dependent on the nucleus, where CD34+ cells revealed to be stiffer than BMSCs for short times under loading assuming elastic behavior and highly viscoelastic for longer times under loading, which present a higher nuclear volume per cell volume ratio. Mechanics was also evaluated for agglomerates of stem cells by aspirating spheres of neural progenitor cells (NSC-Ss). Relatively to single cells, NSC-Ss presented higher deformability, which seems to be more dependent on intracellular connectivity than on cell mechanics. The general character of the reported conclusions is being investigated with other types of stem cells.