Abstract: Objective To induce bone marrow-derived mesenchymal stem cells (BM-MSCs) to differentiate into kidney organoids. Methods By regulating CHIR99021 and FGF9, BM-MSCs were used to differentiate into the kidney organoids. Kidney organoids were treated with immunofluorescence staining. Then electron microscope was used to observe the structure of the kidney organoids. Results By regulating CHIR99021 and FGF9, we have generated the kidney organoids from BM-MSCs successfully. Within these kidney organoids, single renal unit segmented into distal tubules, proximal tubules and glomeruli, which contained podocytes and blood vessels. Conclusion Such kidney organoids generated from BM-MSCs represent powerful models of the human organ which can be used for future clinical research, including nephrotoxicity screening, disease modelling and kidney scaffolds recellularising.