In the last decade Mesenchymal Stem Cells (MSC) are being used more extensively in regenerative medicine. This is due to their ability to differentiate into various cells and due to their extensive paracrine function. They have been successfully isolated from almost every type of tissue, the problem, however, lies in their small numbers and the lack of standardised procedures to determine MSC concentration in freshly isolated samples. The aim of our research was to introduce a procedure for counting MSC in the samples of bone marrow, stimulated peripheral blood and fat tissue with a flow cytometer, using antibodies against cell markers CD271, CD45 and florescent beads for precise cell count. After introducing the procedure, we successfully compared our results with the test determining the count of colony-forming units - fibroblasts (CFU-F). At the same time, we used the samples to determine the concentration of haematopoietic progenitor cells. The highest concentration of MSC was found in the sample of fat tissue, the lowest in those of peripheral blood. Unlike the concentration of haematopoietic progenitor cells and the count of CFU-F, the corelation between the concentration of MSC and the age of the donor samples was statistically insignificant. To get more conclusive results, we should expand our research to a larger group of donors from many different age groups.