Abstract <p>A comparative in vivo analysis was conducted to evaluate the biodistribution efficiency of cells and microvesicles labeled with fluorescent proteins. Mesenchymal stem cells (MSCs) were genetically modified using a recombinant lentivirus carrying the gene for the fluorescent protein Katushka2S, with the goal of labeling both the cells and their derived microvesicles (MVs). The selection of genetically modified MSCs was performed through cell sorting using a FACS Aria III flow cytometer–sorter. The biodistribution of the cells was assessed by detecting the fluorescent signal using the IVIS Spectrum system. Intravenous administration of 5 × 10⁵ MSC-Katushka2S in mice was insufficient for in vivo detection of cell biodistribution. Ex vivo analysis revealed that immediately after intravenous administration, the MSCs accumulated in the lungs and liver. The intensity of Katushka2S protein fluorescence and the sensitivity of the IVIS Spectrum system were sufficient for ex vivo visualization of MSC-Katushka2S cell clusters. However, the quantity of MVs-Katushka2S isolated from 1.5 × 10⁶ MSC-Katushka2S was insufficient for the detection of MV biodistribution both in vivo and ex vivo. Therefore, the application of this method for evaluating the biodistribution of individual cells and microvesicles in vivo is ineffective.</p>