Mesenchymal stem cells (MSCs) are currently defined as cells that undergo sustained in vitro growth and can give rise to multiple mesenchymal lineages. Traditional MSCs isolation methods require prolonged in vitro culture on plastic plates, which reduces their differentiation potential and proliferative ability. Furthermore, this process alters MSCs-phenotype, making it difficult to identify specific MSCs-markers that could be used for their in vivo localization and prospective isolation. These limitations have hindered investigations into the biology and function of MSCs. This review article focuses on recent developments in the MSC-research field including the identification of novel surface markers for the prospective isolation of both murine and human MSCs. Prospectively isolated MSCs are more proliferative than MSCs prepared by conventional plastic adherence, provide a better substrate for studying MSCs biology and have more potential for regenerative therapy.