A new method is introduced for water-fat imaging. With three acquisitions, a general direct phase encoding (DPE) of the chemical shift information is achieved. Pixels containing both water and fat are solved directly. Pixels with only a single component are resolved with local and global orientation filters, which use phase information from neighboring pixels. The fact that a single component is more likely to be water than fat in living tissues is also useful. A second pass solution yields water and fat images with superior signal-to-noise ratio. Unlike other methods, DPE does not rely on the error-prone phase unwrapping; also, it easily handles disconnected tissues. Because the magnetization vectors of water and fat are sampled not only at parallel or antiparallel, they can be not only separated but also identified respectively, which is desirable for routine clinical work. DPE has been implemented on several imagers at various field strengths and has been demonstrated in a large number of clinical cases to be useful and robust in various parts of the body.