We investigated the utility of comprehensive scoring systems for organ failure compared with the duration of extracorporeal life support (ECLS) in predicting survival after heart transplantation. From November 2004 to August 2013, 25 adult patients ultimately underwent heart transplantation while on ECLS. We did not include patients who were younger than 18 years old or patients with extracorporeal ventricular assist devices. Seven patients (28%) died within 1 year after transplantation. The areas under the curve (receiver operating characteristics (ROC), optimal cut-off value) of the sequential organ-failure assessment and the model for end-stage liver disease score modified by the United Network for Organ Sharing scores were 0.794 (13) and 0.825 (24), respectively. In multivariate analysis, the model for end-stage liver disease score modified by the United Network for Organ Sharing score was independently prognostic regardless of the duration of ECLS and sequential organ-failure assessment score.