The term mesenchymal stem cell (MSCs) was adopted in the 1990s to describe a population of bone-marrow-derived cells that demonstrated the capacity for tri-lineage differentiation at a clonal level. Research conducted during the ensuing decades has demonstrated that MSCs fulfill many functions in addition to connective tissue progenitors including contributing to the HSC niche and regulating the function of immune effector cells of both the innate and adaptive immune system. Despite these advances, fundamental aspects of MSC biology remain indeterminate. For example, the embryonic origin of MSCs and their niche in vivo remains a highly debated topic. More importantly, the mechanisms that regulate self-renewal and lineage specification have also been largely unexplored. The later is significant in that MSC population's exhibit considerable donor-to-donor and intra-population heterogeneity but knowledge regarding how different functional attributes of MSCs are specified at the population level is unknown. This poses significant obstacles in research and in efforts to develop clinical manufacturing protocols that reproducibly generate functionally equivalent MSC populations. Herein, I discuss data demonstrating that MSC populations are intrinsically heterogeneous, elaborate on the molecular basis for this heterogeneity, and discuss how heterogeneity impacts clinical manufacturing and the therapeutic potency of MSCs. J. Cell. Biochem. 113: 2806–2812, 2012. © 2012 Wiley Periodicals, Inc.