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The primary goal of this work was to develop and evaluate a new method for simultaneous 3D motion estimation and image reconstruction for gated cardiac emission computed tomography (ECT). The method, termed the MR algorithm, employs a two-step, iterative procedure. The method was evaluated using both simulated and physical phantoms designed to mimic myocardial perfusion imaging in ECT. In both the simulated and physical phantom studies, the images reconstructed by the MR algorithm showed improved noise characteristics relative to a standard iterative algorithm. The percent error of the motion estimate ranged from 16% to 60% for the simulated phantom study, and 40% to 74% for the physical phantom study, depending on the position within the myocardium.