The purpose of this work was to validate a subtraction method for dynamic contrast-enhanced magnetic resonance volumes acquired at portal and delayed (3 hours) phases, to obtain a better depiction and delineation of hepatic secondary lesions. As the clinical readability of subtraction images depends on the degree of co-registration between volumes, we applied a 3D non-rigid registration procedure to realign portal and delayed-phase volumes before subtraction. Our method combines a rigid registration, based on Normalized Mutual Information maximization and a non-rigid registration, based on a multiresolution analysis performed through Wavelet Transform. The feasibility of the method was tested on thirty-five secondary lesions. Results showed that the proposed subtraction produces images of easy interpretation and improves diagnostic confidence. In particular, subtraction image of subcentimetric lesions was scored as diagnostic in the 89% of the cases.