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Computed tomography (CT) and magnetic resonance imaging (MRI) can quantify muscle mass and quality. However, it is still unclear if CT and MRI derived measurements can be used interchangeable. In this prospective study, fifty consecutive participants of a cancer screening program underwent same day low-dose chest CT and MRI. Cross-sectional areas (CSA) of the paraspinal skeletal muscles were obtained. CT and MRI muscle fat infiltration (MFI) were assessed by mean radiodensity in Hounsfield units (HU) and proton density fat fraction (MRI^PDFF), respectively. CSA and MFI were highly correlated between CT and MRI (CSA: r = 0.93, P < 0.001; MFI: r = − 0.90, P < 0.001). Mean CSA was higher in CT compared to MRI (46.6cm² versus 43.0cm²; P = 0.05) without significance. Based on MRI^PDFF, a linear regression model was established to directly estimate skeletal muscle fat content from CT …