Mesenchymal stem cells (MSC) exhibit a high self-renewal capacity, multilineage differentiation potential and immunomodulatory properties. This set of exceptional features makes them an attractive tool for research and clinical application. However, MSC are far from being a uniform cell type, which makes standardization difficult. The exact properties of human MSC (hMSC) can vary greatly depending on multiple parameters including tissue source, isolation method and medium composition. In this review we address the most important influence factors. We highlight variations in the differentiation potential of MSC from different tissue sources. Furthermore, we compare enzymatic isolation strategies with explants cultures focusing on adipose tissue and umbilical cords as two relevant examples. Additionally, we address effects of medium composition and serum supplementation on MSC expansion and differentiation. The lack of standardized methods for hMSC isolation and cultivation mandates careful evaluation of different protocols regarding efficiency and cell quality. MSC characterization based on a set of minimal criteria defined by the International Society for Cellular Therapy is a widely accepted practice, and additional testing for MSC functionality can provide valuable supplementary information. The MSC secretome has been identified as an important signaling mechanism to affect other cells. In this context, extracellular vesicles (EVs) are attracting increasing interest. The thorough characterization of MSC-derived EVs and their interaction with target cells is a crucial step toward a more complete understanding of MSC-derived EV functionality. Here, we focus on flow cytometric approaches to characterize free as well as cell bound EVs and address potential differences in the bioactivity of EVs derived from stem cells from different sources. © 2017 International Society for Advancement of Cytometry.