Transplantation of mesenchymal stem cells (MSCs) has been used to treat a wide range of diseases, and the mechanism of action is postulated to be mediated by either differentiation into functional reparative cells that replace injured tissues, or secretion of paracrine factors that promote tissue repair. To complement earlier studies that identified some of the paracrine factors, we profiled the paracrine proteome to better assess the relevance of MSC paracrine factors to the wide spectrum of MSC-mediated therapeutic effects. To evaluate the therapeutic potential of MSC paracrine proteome, a chemically defined serum-free culture media was conditioned by MSCs derived from human embryonic stem cell (ESC) using a clinically compliant protocol. The conditioned media was analyzed by multidimensional protein identification technology (MuDPIT) and cytokine antibody array analysis, and revealed the presence of 201 unique gene products. 86-88% of these gene products have detectable transcript levels by microarray or qRT-PCR assays. Computational analysis predicted that these gene products will significantly drive three major groups of biological processes: metabolism, defense response, and tissue differentiation including vascularization, hematopoiesis and skeletal development. It also predicted that the 201 gene products activate important signalling pathways in cardiovascular biology, bone development and hematopoiesis such as Jak-STAT, MAPK, Toll-like receptor, TGF-beta signalling and mTOR signaling pathways. This study identified a large number of MSC secretory products that have the potential to act as paracrine modulators of tissue repair and replacement in diseases of the cardiovascular, hematopoietic and skeletal tissues. Moreover, it suggests that hESC-derived MSC conditioned medium has the potency to treat a variety of diseases in humans without cell transplantation.