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While neurological manifestations are core features of Fabry disease (FD), quantitative neuroimaging biomarkers allowing to measure brain involvement are lacking. We used deep learning and the brain‐age paradigm to assess whether FD patients' brains appear older than normal and to validate brain‐predicted age difference (brain‐PAD) as a possible disease severity biomarker. MRI scans of FD patients and healthy controls (HCs) from a single Institution were, retrospectively, studied. The Fabry stabilization index (FASTEX) was recorded as a measure of disease severity. Using minimally preprocessed 3D T1‐weighted brain scans of healthy subjects from eight publicly available sources (N = 2160; mean age = 33 years [range 4–86]), we trained a model predicting chronological age based on a DenseNet architecture and used it to generate brain‐age predictions in the internal cohort. Within a linear modeling framework, brain‐PAD was tested for age/sex‐adjusted associations with diagnostic group (FD vs. HC), FASTEX score, and both global and voxel‐level neuroimaging measures. We studied 52 FD patients (40.6 ± 12.6 years; 28F) and 58 HC (38.4 ± 13.4 years; 28F). The brain‐age model achieved accurate out‐of‐sample performance (mean absolute error = 4.01 years, R2 =.90). FD patients had significantly higher brain‐PAD than HC (estimated marginal means: 3.1 vs. −0.1, p =.01). Brain‐PAD was associated with FASTEX score (B = 0.10, p =.02), brain parenchymal fraction (B = −153.50, p =.001), white matter hyperintensities load (B = 0.85, p =.01), and tissue volume reduction throughout the brain. We demonstrated that FD patients' brains appear older than normal. Brain‐PAD correlates with FD‐related multi‐organ damage and is influenced by both global brain volume and white matter hyperintensities, offering a comprehensive biomarker of (neurological) disease severity. [ABSTRACT FROM AUTHOR]