An improved pulse sequence for the 3D DOSY experiment 2DJ-DOSY, using diffusion encoding internal to the parent 2DJ spectroscopy sequence (2DJ-IDOSY), is presented. The diffusion-encoding pulses are used to enforce the desired coherence transfer pathway, reducing the minimum experimental time by at least a factor of 4, as compared to existing techniques, and approximately doubling the signal-to-noise ratio for small molecules. The new sequence is demonstrated on a simple mixture and on a complex sample with a high dynamic range (port wine). The principle of internal diffusion encoding can be applied with profit to a range of other 3D DOSY experiments.