The perpetual organ shortage crisis worldwide has meant a paradigm shift in global thinking with subsequent expansion of the accepted criteria for an organ donor to meet the demand. Robust pre-transplant organ viability assessment is the next great challenge in the field of transplantation today. Organ preservation in the nature of static cold storage has reached its limits, and machine perfusion both cold and warm offers theoretically superior preservation and the potential to assess organs. Microdialysis is a novel technique with proven ability to allow remote assessment of tissue biochemistry and metabolism. It has been used in various pre-clinical and clinical models of abdominal organ preservation and transplantation. This review focuses on the use of microdialysis in the assessment of the kidney, liver, and pancreas, and where this novel technology is heading in the context of the assessing organ viability prior to and after transplantation.