PurposeTo introduce a new method for motion‐insensitive 3D multishot diffusion imaging using 3D spiral‐encoded navigators from stimulated echoes (3D‐DISPENSE).MethodsThe 3D‐DISPENSE sequence contains a 3D stack‐of‐spiral navigator generated between the diffusion preparation and the turbo spin‐echo image acquisition from the twin pathway of a stimulated echo. Unlike normal navigator methods, 3D‐DISPENSE separates the navigator acquisition from the imaging readout without compromising the image SNR. Phase information from the navigators was included in an iterative image reconstruction algorithm to correct for intershot phase incoherence caused by motion.ResultsIn a phantom experiment, 3D‐DISPENSE correctly estimated deliberately introduced phase errors. In a moving phantom, motion‐induced artifacts in the DWI were greatly mitigated by 3D‐DISPENSE. The ADC after 3D‐DISPENSE correction was identical to the reference. In a brain diffusion tensor experiment, phase‐incoherence artifacts from breathing, cardiac, and subject motion were removed almost perfectly in all view angles, resulting in distortion‐free DWI and color‐coded fractional anisotropy maps with 1.5‐mm isotropic resolution and nearly full brain coverage.ConclusionThree‐dimensional DISPENSE corrects motion‐induced phase‐incoherence artifacts in 3D multishot diffusion imaging and produces high‐quality 3D DWI and DTI.