Purpose: To investigate the feasibility of using IDEAL (Iterative Decomposition with Echo Asymmetry and Least squares estimation) fat-water imaging and the resultant fat fraction metric in detecting brown adipose tissue (BAT) in mice, and in differentiating BAT from white adipose tissue (WAT). Materials and Methods: Excised WAT and BAT samples and whole-mice carcasses were imaged with a rapid three-dimensional fat-water IDEAL-SPGR sequence on a 3 Tesla scanner using a single-channel wrist coil. An isotropic voxel size of 0.6 mm was used. Excised samples were also scanned with single-voxel proton spectroscopy. Fat fraction images from IDEAL were reconstructed online using research software, and regions of WAT and BAT were quantified. Results: A broad fat fraction range for BAT was observed (40-80%), in comparison to a tighter and higher WAT range of 90-93%, in both excised tissue samples and in situ. Using the fat fraction metric, the interscapular BAT depot in each carcass could be clearly identified, as well as peri-renal and inguinal depots that exhibited a mixed BAT and WAT phenotype appearance. Conclusion: Due to BAT's multi-locular fat distribution and extensive mitochondrial, cytoplasm, and vascular supply, its fat content is significantly less than that of WAT. We have demonstrated that the fat fraction metric from IDEAL-MRI is a sensitive and quantitative approach to noninvasively characterize BAT. © 2010 Wiley-Liss, Inc.