To explore the utility of two different fat quantification methods in the liver and pancreas and to test the accuracy of multi-echo Dixon as a single sequence in detecting early stage of fat deposition. 58 healthy potential liver donors underwent abdominal 3T MRI, prospectively. Single-voxel MR Spectroscopy (MRS), dual-echo Dixon, and multi-echo Dixon were performed. Two independent readers obtained proton density fat fraction (PDFF) of the liver and pancreas by placing ROIs on the 2 Dixon sequences. Correlation between the two PDFF measurements was assessed in the liver and pancreas. Values in the liver were also compared to those obtained by MRS. PDFF in the liver was 6.3 ± 4.2%, 5.5 ± 3.9%, and 5.1 ± 4.1% by MRS, dual-echo Dixon, and multi-echo Dixon, respectively. Dual-echo Dixon and multi-echo Dixon showed good correlation in PDFF quantification of the liver (r = 0.82, p < 0.0005). Multi-echo Dixon showed a good correlation (r = 0.72, p = 0.0005) between the fat measured in the liver and in the pancreas. To differentiate between normal (PDFF ≤ 6%) and mild fat deposition (PDFF: 6-33%) in the liver, analysis showed sensitivity, specificity, and accuracy of 74%, 81%, and 80% for dual-echo Dixon and 85%, 96%, and 89% for multi-echo Dixon, respectively. Mean PDFF in the pancreas was 7.2 ± 2.8% and 6.7 ± 3.3%, by dual-echo and multi-echo Dixon, respectively. Dual-echo Dixon and multi-echo Dixon showed good correlation in PDFF quantification of the pancreas (r = 0.58, p < 0.0005). Multi-echo Dixon in liver has high accuracy in distinguishing between subjects with normal liver fat and those with mildly elevated liver fat. Multi-echo Dixon can be used to screen for early fat deposition in the liver and pancreas.