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Background Quantification of volume and inflammatory activity in the fat tissue is important because these are closely related to type 2 diabetes mellitus and cardiovascular disease. Fluorine-18 fluorodeoxyglucose (F-FDG) PET/computed tomography (CT) has been utilized to measure the metabolic activity of fat tissue. In this study, we assessed the feasibility of simultaneous PET/magnetic resonance (MR) in metabolic and volumetric measurements of fat tissue and the potential advantage over PET/CT. Methods Twenty-four healthy individuals were enrolled, who underwent simultaneous F-FDG PET/MRI. Twenty-five F-FDG PET/CT scans were selected. Isocontour volumes of interest (VOIs) were used to segment and separate visceral fat (VF) and abdominal subcutaneous fat (SF) in using the MR image (T1 DIXON VIBE sequence) of PET/MR and the CT image of PET/CT. Volume, mean standardized uptake value of VF, and SF VOIs were calculated. Results Overlap between F-FDG PET and VF VOI was better in F-FDG PET/MR than PET/CT. The mean standardized uptake value of VF was associated with the degree of intestinal uptake on F-FDG PET/CT, but not on F-FDG PET/MR. Volumetric and metabolic measurements using F-FDG PET/MR showed an excellent reproducibility, with a high intraclass correlation coefficient between different observers (0.951-0.997). The measured metabolic activity was higher in VF than SF. Conclusion We established a method for the quantitative measurement of volume and metabolic status of abdominal VF and SF using simultaneous F-FDG PET/MR. F-FDG PET/MR has an advantage over F-FDG PET/CT in terms of being less confounded by intestinal uptake. This method could be used to assess the inflammatory activity of fat tissue, which is a major risk factor for type 2 diabetes mellitus and cardiovascular disease.