The transplant center regulations recently published by the Centers for Medicare and Medicaid (CMS) mandate that observed program-specific survival outcomes to fall within expected risk-adjusted outcomes. Meeting these outcomes is essential to continued participation in the Medicare program. Both donor and recipient variables not considered in current risk adjustment models can result in inferior outcomes and therefore may cause an overestimation of transplant center expected performance, precluding participation in the federally funded Medicare program. We reviewed the most recent four reporting periods published by the Scientific Registry for Transplant Recipients on their public website. We identified kidney, liver and heart transplant programs that were flagged for having outcomes statistically lower than expected as well as those that failed to meet CMS criteria. We also analyzed whether center volumes correlated with outcomes in these centers. We highlight the need for mitigating factors that could justify inferior outcomes under specific circumstances. Failure to reach consensus on such a mechanism for appeal may result in risk-averse behavior by transplant centers with respect to innovation and therefore hamper the ability to advance the field of transplantation. We propose a methodology that may address this emerging dilemma.