The lung allocation score system in the United States and several European countries gives more weight to risk of death without transplantation than to survival following transplantation. As a result, centers transplant sicker patients, leading to increased length of initial hospitalization. The care of patients who have accumulated functional deficits or additional organ dysfunction during their prolonged stay can be ethically complex. Disagreement occurs between the transplant team, patients and families, and non-transplant health care professionals over the burdens of ongoing intensive intervention. These cases highlight important ethical issues in organ transplantation, including the nature and requirements of transplant informed consent, the limits of physician prognostication, patient autonomy and decision-making capacity following transplant, obligations to organ donors and to other potential recipients, and the impact of program metrics on individualized recipient care. We outline general ethical principles for the care of lung transplant recipients with prolonged hospitalization and give regulatory, research, and patient-centered recommendations for these cases.