We evaluated dual-echo Dixon in-phase and out-of-phase (IP-OP), chemical shift imaging (CSI), and (1)H MRS (hydrogen MR spectroscopy) in estimating fat content (FC) in phantoms and in livers of mice. Phantoms were made according to the volume percentage of fat ranging from 0% to 100%. The three MR methods were performed to measure FC in phantoms and in livers of obese leptin-deficient (ob/ob), human BSCL2/seipin gene knockout (SKO), and wild-type (WT) mice. The results were compared with known FC in phantoms and to a reference standard from mice by histological semiautomatic vacuole segmentation (HIS-S) procedure and liver lipid (LL) chemical analysis. In phantoms, CSI underestimated FC from 50% to 100%, to a lesser extent than IP-OP. In vivo, liver FC in ob/ob and SKO mice measured by the three MR methods were all significantly higher than that in WT mice. Liver FC measured by IP-OP were significantly lower than that measured by CSI and MRS, with no significant difference between CSI and MRS. CSI and MRS showed a linear correlation with LL analysis and with each other. IP-OP underestimated FC, whereas CSI and MRS were more accurate for quantifying FC in both phantoms and liver. CSI and MRS have the potential to replace HIS-S and LL analysis in longitudinal studies.