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A precise prognosis is of imminent importance in intensive care medicine. This article provides data showing the overestimation of intrahospital mortality by APACHE II score in various subgroups of cardiogenic shock patients treated with a percutaneous left ventricular assist device. The data set includes additional baseline characteristics regarding age, pre-existing diseases, characteristics of coronary artery disease, characteristics of cardiopulmonary resuscitation, and hemodynamic parameter not included in the APACHE II score. Further data were provided which characterize derivation and validation group. Both groups were used for adjustment of the APACHE II approach. The data are supplemental to our original research article titled “Predictive value of the APACHE II score in cardiogenic shock patients treated with a percutaneous left ventricular assist device” (Mierke et al., IJC Heart & Vasculature. 40 (2022) 101013. https://doi.org/10.1016/j.ijcha.2022.101013).