A method for reducing mis-registration during multiple energy scanning on computed tomographic (CT) imaging systems or multiple energy electron beam tomographic (EBT) systems includes scanning a portion of a patient including a cyclically moving body part using a multiple energy computed tomographic (CT) imaging system or multiple energy electron beam tomographic (EBT) system having at least two different energies, monitoring the cyclically moving body part, and gating the multiple energy CT imaging system or multiple energy EBT system in accordance with the monitored cyclically moving body part so that acquisitions are acquired at at least two different kVps. The data acquired at the different kVps are then utilized to generate material decomposition images of the cyclically moving body part.