Institutional review board approval was obtained for multiple imaging examinations in healthy volunteers and patients and for the analysis of images. The purpose of the study, and the risks associated with radiation exposure with regard to stochastic effects that might result in cancer and/or genetic mutations, were explained to all subjects, and all questions from subjects were answered. Each subject provided written informed consent. The purpose of the study was to prospectively determine the respiratory protocol at computed tomography (CT) that results in the best registration of CT images with images acquired at single photon emission computed tomography (SPECT) in the thorax. Errors of registration between myocardial SPECT images and CT images obtained with different respiratory protocols (postinhalation breath hold, postexhalation breath hold, and free breathing) in 13 healthy subjects were compared. CT scans obtained with free breathing and postexhalation breath hold better matched SPECT images than did those obtained with postinhalation breath hold (one-way analysis of variance, P < .01). Fewer SPECT/CT images showed artifacts with registration performed by using internal landmarks (four, two, and one of 13 images with postinhalation breath-hold, postexhalation breath-hold, and free-breathing protocols, respectively) than with registration performed by using external markers (nine, four, and two of 13 images). CT data acquisition with a free-breathing or postexhalation breath-hold protocol and image registration by using internal landmarks are recommended for attenuation correction.