Large area detector computed tomography systems with fastrotating gantries enable volumetric dynamic cardiac perfusion studies. Prospectively ECG-triggered acquisitions limit the data acquisition to a predefined cardiac phase and thereby reduce X-ray dose andlimit motion artifacts. Even in the case of highly accurate prospective triggering and stable heart rate, spatial misalignment of the cardiac volumes acquired and reconstructed per cardiac cycle may occurdue to small motion pattern variations from cycle to cycle. These misalignments reduce the accuracy of the quantitative analysis of myocardial perfusion parameters on a per voxel basis. An image based solution to this problem is elastic 3D image registration of dynamic volume sequences with variable contrast, as it is introduced in thiscontribution. After circular cone-beam CT reconstruction of cardiacvolumes covering large areas of the myocardial tissue, the completeseries is aligned with respect to a chosen reference volume. The results of the quantitative perfusion analysis are compared on pig datausing the non-registered versus the registered data set. The reduced spatial misalignment leads to an improved characterization of myocardial perfusion confirming the potential of this method. Conclusions - In conclusion, an elastic image registration-based method was proposed to improve the characterization of CT-based estimates of myocardial perfusion. The techniques performance, that was visually and quantitatively assessed on three pig data sets, confirmed its potential. The proposed method may also be applied to other perfusion studies being limited by inconsistent motion states.