Purpose To evaluate the reliability of quantitation of myocardial viability on cardiac F-18 fluorodeoxyglucose (FDG) positron emission tomography (PET) scans with three different methods of visual scoring system, autoquantitation using commercially available autoquantitation software, and infarct-size measurement using histogram-based maximum pixel threshold identification on polar-map in rat hearts. Methods A myocardial infarct (MI) model was made by left anterior descending artery (LAD) ligation in rat hearts. Eighteen MI rats underwent cardiac FDG-PET-computed tomography (CT) twice within a 4-week interval. Myocardium was partitioned into 20 segments for the comparison, and then we quantitated non-viable myocardium on cardiac FDG PET-CT with three different methods: method A-infarct-size measurement using histogram-based maximum pixel threshold identification on polar-map; method B-summed MI score (SMS) by a four-point visual scoring system; method C-metabolic non-viable values by commercially available autoquantitation software. Changes of non-viable myocardium on serial PET-CT scans with three different methods were calculated by the change of each parameter. Correlation and reproducibility were evaluated between the different methods. Results Infarct-size measurement, visual SMS, and nonviable values by autoquantitation software presented proportional relationship to each other. All the parameters of methods A, B, and C showed relatively good correlation between each other. Among them, infarct-size measurement (method A) and autoquantitation software (method C) showed the best correlation (r=0.87, p<0.001). When we evaluated the changes of non-viable myocardium on the serial FDG-PET-CT-however, autoquantitation program showed less correlation with the other methods. Visual assessment (method B) and those of infarct size (method A) showed the best correlation (r=0.54, p=0.02) for the assessment of interval changes. Conclusions Commercially available quantitation software could be applied to measure the myocardial viability on small animal cardiac FDG-PET-CT scan. This kind of quantitation showed good correlation with infarct size measurement by histogram-based maximum pixel threshold identification. However, this method showed the weak correlation when applied in the measuring the changes of non-viable myocardium on the serial scans, which means that the caution will be needed to evaluate the changes on the serial monitoring.