We present a method of labeling of mesenchymal stem cells from human amnion with a fluorescent dye Dil and microspheres (Bangs Laboratories). The possibility of administration of loaded cell culture was verified and comparative analysis of the phenotype of mesenchymal stem cells by the expression of fibronectin, nestin, CD13, CD29, CD34, CD44, CD54, CD90, CD105, CD106, HLA-ABC, HLA-DR, and PCNA was carried out. The labeled cells retained osteogenic differentiation capacity. The results suggest that fluorescent dye Dil and microspheres from Bangs Laboratories can be used for monitoring of mesenchymal stem cells from human amnion in in vivo experiments.