Background The Eurotransplant community adopted an urgency-based heart allocation algorithm in August 2000. The effect of the new allocation policy on critically ill patients with end-stage heart failure was studied. Methods During 1997–1999 (old algorithm) and 2001–2006 (new algorithm), 661 heart transplant candidates received heart transplantation (HTx) or a ventricular assist device (VAD) at our center. Those patients who received VAD or urgent HTx (decompensated) were assigned to Group D-97 ( n = 108) and Group D-01 ( n = 307) under the old and new algorithm, respectively, and regarded as critically ill. We defined subgroups of critically ill patients as follows: Group VAD-97 ( n = 92) and Group VAD-01 ( n = 184), who underwent primary VAD implantation under the old and new allocation algorithm, respectively; and Group UTx-97 ( n = 16) and Group UTx-01 ( n = 123), who underwent urgent HTx under the old and new algorithm. Group survival rates were studied. Results Group D-01 had significantly higher survival rates than D-97 (61.7% vs 44.4%, 2-year survival; p < 0.001). The ratio of patients with urgent HTx (Group UTx-01) among the patients in Group D-01 was significantly greater than that in Group D-97 (40.1% vs 14.8%, p < 0.001). Survival rates of Group UTx-01 after urgency listing (71.5% for 2-year survival) were significantly better than those after VAD implantation in Groups VAD-01 and VAD-97. Conclusions The new heart allocation algorithm has successfully improved survival rates of critically ill patients, enabling these patients to receive urgent HTx.