There is considerable interest among basic and clinical scientists in exploiting the remarkable therapeutic potential of the stem cells from bone marrow referred to as mesenchymal stem cells or MSCs. The relative ease of MSC procurement and promising results obtained with the cells in models for human disease has encouraged their use in numerous clinical trials. Traditionally, MSCs have been expanded as 2D adherent cultures on plastic surfaces. As stem cells in their native form exist in specialized micro-environments or ‘niches’ the concept that 3D culture approaches could enhance the therapeutic benefits of the cells is of recent interest. The premise behind this hypothesis is that 3D culture recapitulates the spatial organization of the stem cell niche and promotes appropriate intercellular and cell-matrix interactions. These relationships modulate gene expression patterns and can therefore influence cell differentiation and function. Currently, this research laboratory is engaged in the development of 3D culture systems for MSCs to pre-activate the cells and better utilize their inherent therapeutic potential often overshadowed by the limitations of conventional culture methods. The properties of MSCs derived from 3D cultures regarding the ability of the cells to home to injured tissues, reduce inflammation, modulate immune function, suppress tumor growth, and activate tissue-resident stem cells are all under investigation. Moreover, this group aims to determine the cellular and molecular cues that drive the therapeutic effects of MSCs.