The recognition that adult bone marrow stem cells (BMSCs) can traffic into the liver and kidney and differentiate into a variety of cell types such as epithelial cells, endothelial cells and myofibroblasts has caused excitement. This has expanded our knowledge of how these organs regenerate following damage and provides new opportunities for therapeutic exploitation. BMSC transplants have already been used to correct a murine model of metabolic liver disease. Bone marrow stem cells that transdifferentiate into long-lasting cells within the liver and kidney are proposed as suitable targets for gene therapy and may be used in the correction of single gene defects, or the delivery of antiviral and anti-inflammatory genes to the liver and kidney. There is growing evidence that BMSCs can repopulate the endothelium of transplanted livers and kidneys and thus may potentially be manipulated to induce graft tolerance within solid organ transplants. However, there are technical barriers to be overcome before the theoretical benefits of this exiting new area becomes a practical prospect.