Distinguishing between lipid and water-containing tissues is clinically important. Current techniques rely on the chemical shift difference between fat and water resonances or differences in relaxation times of the tissues, or a combination of both. A method is presented for separating the signals of lipid protons from those of water protons by using fast spin-echo magnetic resonance imaging based on the principle that lipid protons behave differently from water protons in multi-echo sequences. Two images are acquired with different echo train lengths and echo spacing but with identical TEs, and then subtracted to exploit differences in the behavior of lipid and water protons in multi-echo sequences. The method is insensitive to B0 inhomogeneities or susceptibility effects and provides separate lipid and water images with a high signal-to-noise ratio. The advantages of the method are demonstrated with phantom studies and clinical examples.