Recent studies have shown promising results using ¹⁸F-fluorodeoxyglucose positron emission tomography/computed tomography (¹⁸F-FDG PET/CT) in the diagnosis of prosthetic valve endocarditis (PVE). However, previous studies did not include negative controls. The aim of this study was to compare ¹⁸F-FDG-uptake around prosthetic aortic valves in patients with and without PVE and to determine the diagnostic performance of ¹⁸F-FDG PET/CT in the diagnosis of PVE. ¹⁸F-FDG PET/CT examinations in patients with a prosthetic aortic valve performed 2008–2014 were retrieved. Eight patients with a final diagnosis of definite PVE were included in the analysis of the diagnostic performance of ¹⁸F-FDG PET/CT. Examinations performed on suspicion of malignancy in patients without PVE (n = 19) were used as negative controls. Visual and semi-quantitative analysis was performed. Maximal standardized uptake value (SUV_max) in the valve area was measured and SUV_ratio was calculated by dividing valve SUV_max by SUV_max in the descending aorta. The sensitivity was 75 %, specificity 84 %, positive likelihood ratio [LR(+)] 4.8 and negative likelihood ratio [LR(−)] 0.3 on visual analysis. Both SUV_max and SUV_ratio were significantly higher in PVE patients [5.8 (IQR 3.5–6.5) and 2.4 (IQR 1.7–3.0)] compared to non-PVE patients [3.2 (IQR 2.8–3.8) and 1.5 (IQR 1.3–1.6)] (p < 0.001). ROC-curve analysis of SUV_ratio yielded an area under the curve of 0.90 (95 % CI 0.74–1.0). ¹⁸F-FDG-uptake around non-infected aortic prosthetic valves was low. The level of ¹⁸F-FDG-uptake in the prosthetic valve area showed a good diagnostic performance in the diagnosis of PVE.