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Mesenchymal stem cells (MSCs) are pluripotent cells that can differentiate into endothelial, osteogenic, adipogenic, and other lineages. In spite of the broad interest, little is known about the variation of MSC number in relation to the age of the donor. The aim of this study was to investigate the age-associated variations of bone marrow (BM) MSCs using a rat model. Cell populations were characterized by flow cytometry using light-scattering parameters, DNA content and a set of monoclonal antibodies and detected by magnetic resonance imaging (MRI). Single-cell analysis was performed by conventional fluorescent microscopy. BM mononucleated cells (MNCs) were isolated, in vitro culture of MSCs was established, and endothelial cells differentiation and intracellular magnetic labeling was shown. The amount of BM tissue obtainable from femurs and tibiae increased with age and reached a maximum in 8- to 12-week-old rats. At the same time, the proportional number of MNCs containing MSCs decreased. As a result, after 2 weeks of culture, the maximum yield of MSC number was registered from the youngest age group (4 weeks). MSCs were differentiated into endothelial cells by administration of vascular endothelial growth factor (VEGF) and subsequently revealed immunocytochemical and morphological characteristics of endothelial cells. The results of our study are the basis for further experiments with MSCs and their endothelial descendants, which may be labeled with different agents for cell tracking and detection experiments, but age-related changes in MSCs number should be taken into account whenever these cells are considered for practical applications.