Error-free reconstruction of PET data with a registered CT attenuation map is essential for accurate quantification and interpretation of cardiac perfusion. Misalignment of the CT and PET data can produce an erroneous attenuation map that projects lung attenuation parameters onto the heart wall, thereby underestimating the attenuation and creating artifactual areas of hypoperfusion that can be misinterpreted as myocardial ischemia or infarction. The major causes of misregistration between CT and PET images are the respiratory motion, cardiac motion and gross physical motion of the patient. The misalignment artifact problem is overcome with automated cardiac registration software that minimizes the alignment error between the two modalities. Results show that the automated registration process works equally well for any respiratory phase in which the CT scan is acquired. Further evaluation of this procedure on 50 patients demonstrates that the automated registration software consistently aligns the two modalities, eliminating artifactual hypoperfusion in reconstructed PET images due to PET/CT misregistration. With this registration software, only one CT scan is required for PET/CT imaging, which reduces the radiation dose required for CT-based attenuation correction and improves the clinical workflow for PET/CT.