Metabolic syndrome increases the risk of chronic diseases such as cardiovascular disease and diabetes. Metabolic syndrome also has an impact on bone mineral density. However, the relationship between metabolic syndrome and bone marrow fat is unclear.To determine factors associated with bone marrow fat concentration in subjects with and without metabolic syndrome.Retrospective.One hundred and one women with metabolic syndrome (31.0 years ±5.1) and 96 female living liver transplant donors (32.0 years ±3.7). Our institutional review board approved the study. Each subject signed written informed consent.3.0 T MRI system and a commercially available chemical shift-encoded 3D sequence (Iterative Decomposition of water and fat with Echo asymmetry and Least Square Estimation).Proton density fat fraction (PDFF) in liver, vertebral body, and paraspinal muscle (erector spinae) were measured from a single acquisition by a 15-year-experience orthopedic radiologist. The factors associated with PDFF were acquired.The analysis of covariance test, after adjustment for body mass index and age, was used to analyze the differences between metabolic syndrome and non-metabolic syndrome groups. A stepwise multiple regression analysis was used to determine which variables were independently associated with PDFF.Mean vertebral PDFF and alanine aminotransferase (ALT) were significantly lower in donors than subjects with metabolic syndrome (both P < 0.05). Serum vitamin D concentration, ferritin, and high-density lipoprotein (HDL) cholesterol were significantly higher in donors than subjects with metabolic syndrome (all P < 0.05). Multiple regression analysis revealed antidiabetic medicine, higher serum vitamin D concentration, lower waist circumference, lower ferritin, lower HDL, absence of metabolic syndrome, and lower ALT were significantly associated with lower vertebral PDFF (all P < 0.05).Multiple factors affect bone marrow fat concentration in subjects with metabolic syndrome. Serum vitamin D concentration and antidiabetic medicine are associated with low bone marrow fat, whereas waist circumference, serum ferritin, metabolic syndrome, imbalanced lipid metabolism, and abnormal liver function are associated with high bone marrow fat.3 TECHNICAL EFFICACY STAGE: 1.© 2021 International Society for Magnetic Resonance in Medicine.