We studied the possibility of using different methods for identification of mesenchymal multipotent stromal cells in the renal parenchyma under conditions of experimental thermal ischemia of the kidneys and acute pyelonephritis. In vivo and in vitro methods of identification of mesenchymal multipotent stromal cells by magnetic resonance imaging and immunological and immunohistochemical methods were compared. Labeling of stem cells with iron-containing particles followed by their histological identification and immunohistochemical staining with species-specific antibodies were the most informative methods. Active migration of the cells to the renal tissue was detected by these methods in experimental acute pyelonephritis with inflammation foci.