Chemical exchange saturation transfer (CEST) is a technique to indirectly detect pools of exchangeable protons through the water signal. To increase its applicability to human studies, it is needed to develop sensitive pulse sequences for rapidly acquiring whole‐organ images while adhering to stringent amplifier duty cycle limitations and specific absorption rate restrictions. In addition, the interfering effects of direct water saturation and conventional magnetization transfer contrast complicate CEST quantification and need to be reduced as much as possible. It is shown that for protons exchanging with rates of less than 50–100 Hz, such as imaged in amide proton transfer experiments, these problems can be addressed by using a three‐dimensional steady state pulsed acquisition of limited B1 strength (∼1 μT). Such an approach exploits the fact that the direct water saturation width, magnetization transfer contrast magnitude, and specific absorption rate increase strongly with B1, while the size of the CEST effect for such protons depends minimally on B1. A short repetition time (65 ms) steady‐state sequence consisting of a brief saturation pulse (25 ms) and a segmented echo‐planar imaging train allowed acquisition of a three‐dimensional whole‐brain volume in approximately 11 s per saturation frequency, while remaining well within specific absorption rate and duty cycle limits. Magnetization transfer contrast was strongly reduced, but substantial saturation effects were found at frequencies upfield from water, which still confound the use of magnetization transfer asymmetry analysis. Fortunately, the limited width of the direct water saturation signal could be exploited to fit it with a Lorentzian function allowing CEST quantification. Amide proton transfer effects ranged between 1.5% and 2.5% in selected white and grey matter regions. This power and time‐efficient 3D pulsed CEST acquisition scheme should aid endogenous CEST quantification at both high and low fields. Magn Reson Med, 2011. © 2011 Wiley Periodicals, Inc.