We introduce 3D blip-up and -down acquisition (3D-BUDA) for 3D echo planar imaging (3D-EPI). We acquire two-shots of 3D-EPI with alternating phase-encoding to estimate B0 information. Incorporating this into the joint reconstruction of the shots eliminates distortion and enables signal averaging, permitting a 22-second, high-SNR acquisition at 1 mm3 resolution. While shifted sampling between the shots provides complementary k-space coverage, using low-rank regularization eliminates shot-to-shot variations. SNR gain of 7T allows for additional partition acceleration, enabling a 9-second whole-brain scan at Rinplane×Rz=5×2. These are combined with a self-supervised dipole inversion algorithm for Quantitative Susceptibility Mapping (QSM) which outperforms state-of-the-art reconstructions.