For cardiovascular research on rodents, small-animal PET has limitations because of the inherent spatial resolution of the system and because of cardiac motion. A factor analysis (FA) technique for extracting the blood input function and myocardial time-activity curve from dynamic small-animal PET images of the rodent heart has been implemented to overcome these limitations. Six Sprague-Dawley rats and 6 BALB/c mice underwent dynamic imaging with 18F-FDG (n = 6) and 1-11C-acetate (n = 6). From the dynamic images, blood input functions and myocardial time-activity curves were extracted by the FA method. The accuracy of input functions derived by the FA method was compared with that of input functions determined from serial blood samples, and the correlation coefficients were calculated. Factor images (right ventricle, left ventricle, and myocardium) were successfully extracted for both 18F-FDG and 1-11C-acetate in rats. The correlation coefficients for the input functions were 0.973 for 18F-FDG and 0.965 for 1-11C-acetate. In mice, the correlation coefficients for the input functions were 0.930 for 18F-FDG and 0.972 for 1-11C-acetate. The FA method enables minimally invasive extraction of accurate input functions and myocardial time-activity curves from dynamic microPET images of rodents without the need to draw regions of interest and without the possible complications of surgery and repeated blood sampling.