Conventional, breath-holding magnetic resonance imaging (MRI) assesses body composition by measuring fat volumes and proton density fat fraction (PDFF). However, breath-holding MRI is not always feasible in children. This study's objective was to use free-breathing MRI to quantify visceral and subcutaneous fat volumes and PDFFs and correlate these measurements with hepatic PDFF. This was an observational, hypothesis-forming study that enrolled 2 groups of children (ages 6-17 years), healthy children and overweight children with presumed nonalcoholic fatty liver disease. Free-breathing MRI was used to measure visceral and subcutaneous fat volumes and PDFFs, and hepatic PDFF. Imaging biomarkers were compared between groups, and correlations coefficients (r) and coefficients of determination (R) were calculated. When compared with the control group (n = 10), the overweight group (n = 9) had greater mean visceral (1843 vs 329 cm, P < 0.001) and subcutaneous fat volumes (7663 vs 893 cm, P < 0.001), as well as greater visceral (80% vs 45%, p < 0.001) and subcutaneous fat PDFFs (89% vs 75%, P = 0.003). Visceral fat volume (r = 0.79, P < 0.001) and PDFF (r = 0.92, P < 0.001) correlated with hepatic PDFF. In overweight subjects, for each unit increase in visceral fat PDFF, hepatic PDFF increased by 2.64%; visceral fat PDFF explained 54% of hepatic PDFF variation (R = 0.54, P = 0.02). In this study, we used free-breathing MRI to measure body composition in children. Future studies are needed to investigate the possible value of subcutaneous and visceral fat PDFFs, and validate free-breathing MRI body composition biomarkers.