OBJECTIVE To evaluate the efficiency of mesenchymal stem cells in ameliorating renal scarring in a rat pyelonephritis model. METHODS Three groups each, including 8 Sprague-Dawley rats were formed: Group 1 = sham operated (4 were given mesenchymal stem cells); group 2 = pyelonephritis induced by Escherichia coli; and group 3 = pyelonephritis and mesenchymal stem cells. Rats not given mesenchymal stem cells in group 1 and 4 rats in groups 2 and 3 were sacrificed on the eighth day for evaluation of inflammation, and the remaining rats were sacrificed at the sixth week to determine renal scarring along with migration of mesenchymal stem cells to renal tubules and differentiation to tubular cells expressing aquaporin-1. RESULTS Rats in group 3 had lower scores of both acute (8th day) and chronic (6th week) histopathological alterations compared with rats in group 2. By contrast, although rats in group 3 were shown to have mesenchymal stem cells expressing aquaporin-1 in their renal tubules, these cells were not detected in kidney tissue of mesenchymal stem cells-treated sham rats.