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Abstract Background Metabolic imaging is routinely used to demonstrate aortitis in patients with giant-cell arteritis. We aimed to investigate the preclinical model of aortitis in BALB/c IL1rn −/− mice using [18F]fluorodeoxyglucose ([18F]FDG) positron emission tomography–magnetic resonance (PET-MR), gamma counting and immunostaining. We used 15 first-generation specific and opportunistic pathogen-free (SOPF) 9-week-old IL1rn −/− mice, 15 wild-type BALB/cAnN mice and 5 s-generation specific pathogen-free (SPF) 9-week-old IL1rn −/− . Aortic [18F]FDG uptake was assessed as the target-to-background ratio (TBR) using time-of-flight MR angiography as vascular landmarks. Results [18F]FDG uptake measured by PET or gamma counting was similar in the first-generation SOPF IL1rn −/− mice and the wild-type group (p > 0.05). However, the first-generation IL1rn −/− mice exhibited more interleukin-1β (p = 0.021)- and interleukin-6 (p = 0.019)-positive cells within the abdominal aorta than the wild-type mice. In addition, the second-generation SPF group exhibited significantly higher TBR (p = 0.0068) than the wild-type mice on the descending thoracic aorta, unlike the first-generation SOPF IL1rn −/− mice. Conclusions In addition to the involvement of interleukin-1β and -6 in IL1rn −/− mouse aortitis, this study seems to validate [18F]FDG PET-MR as a useful tool for noninvasive monitoring of aortitis in this preclinical model.