Abstract Background Positron Emission Tomography (PET) uptake allows for the assessment of molecular activity, being 18F-FDG uptake indicative of glucose metabolism. PET uptake is commonly quantified manually by drawing regions of interest, which is subjective, poorly-reproducible and may miss relevant information. Purpose To develop and test an image analysis method to quantify and map 18F-FDG uptake on the whole aortic wall and thrombus. Methods PET-MRI was acquired in patients with thoracic or abdominal aortic aneurysms. The aorta was semi-automatically segmented in the MR angiography using 3DSlicer, generating a surface mesh that was expanded by 3 mm inward and outward. PET uptake was interpolated over this volume with a uniform spatial resolution of 1 mm. By means of 9 reference points, the aortic wall was discretized into 52 (thoracic) or 80 (thoraco-abdominal) standardized regions (i.e. wall patches). For each aortic patch and for the whole thrombus volume, the target to background Ratio (TBR) was calculated by dividing the uptake by a reference uptake in the left atrium. Two observers segmented the aorta and thrombus, located the anatomical reference points and quantified TBR. Inter-observer agreement for segmentation and aortic wall discretization was evaluated in terms of the 95% Hausdorff Distance (HD) and Dice Score Coefficient (DSC), while both median and 95% TBR in each region were tested via intra-class correlation coefficient (absolute value, single measure). Results Data from 20 patients with thoracic or abdominal aneurysms were analysed, 10 of them presented thrombus. The reproducibility of the segmentation of the aorta (median HD 3.16 IQR [2.42 - 3.94] mm, DSC 0.90 [0.89 - 0.92]) and of the thrombus (HD 4.87 [3.51 - 8.45] mm, DSC 0.85 [0.80 - 0.87]) were excellent. The inter-observer agreement in the localization of reference points was good (HD 5.10 [3.29 - 8.73] mm), resulting in excellent overlapping of the standardized aortic wall patches (HD 3.80 [2.44 - 5.08] mm). Inter-observer agreement of median and 95% TBR in each aortic patch were excellent (ICC of 0.90 and 0.93, respectively, Figure 1), with minimal bias (Figure 2). Similarly, excellent interobserver reproducibility was observed for median and 95% TBR in the thrombus (ICC of 0.97 and 0.96, respectively, Figure 2). Conclusions A robust and reproducible image analysis method to map PET uptake along the aortic wall was developed, extending the possibilities to study aortic diseases molecular activity and its association with local aortic characteristics.