Purpose Due to the high morbidity and mortality of infective endocarditis (IE), medical imaging techniques are combined to ensure a correct diagnosis. [18F]FDG PET/CT has demonstrated the ability to improve diagnostic accuracy compared with the conventional modified Duke criteria in patients with suspected IE, especially those with prosthetic valve infective endocarditis (PVIE). The aim of this study is to provide an adjunctive diagnostic tool to improve the diagnostic accuracy in cardiovascular infections, specifically PVIE. Methods A segmentation tool to extract quantitative measures of [18F]FDG PET/CT image studies of prosthetic heart valve regions was developed and validated in 20 cases of suspected PVIE, of which 9 were confirmed. For that, Valvular Heterogeneity Index (VHI) and Ring-to-Center Ratio (RCR) were defined. Results Results show an overall increase in the metabolic uptake of the prosthetic valve ring in the studies with confirmed PVIE diagnosis (SUVmax from 1.70 to 3.20; SUVmean from 0.86 to 1.50). The VHI and RCR showed areas under the curve of 0.727 and 0.808 in the receiver operating characteristics curve analyses, respectively, for PVIE diagnosis. Mann–Whitney U tests showed statistically significant differences between groups for RCR (p = 0.02). Visual analyses and clinical reports were concordant with the extracted quantitative metrics. Conclusion The proposed new method and presented software solution (CASSIA) provide the capability to assess quantitatively myocardial metabolism along the prosthetic valve region in routine [18F]FDG PET/CT scans for evaluating heart valve infectious processes. VHI and RCR are proposed as new potential adjunctive measures for PVIE diagnosis.