PurposeThe gradient‐echo MR signal in brain white matter depends on the orientation of the fibers with respect to the external magnetic field. To map microstructure‐specific magnetic susceptibility in orientationally heterogeneous material, it is thus imperative to regress out unwanted orientation effects.MethodsThis work introduces a novel framework, referred to as microscopic susceptibility anisotropy imaging, that disentangles the 2 principal effects conflated in gradient‐echo measurements, (a) the susceptibility properties of tissue microenvironments, especially the myelin microstructure, and (b) the axon orientation distribution relative to the magnetic field. Specifically, we utilize information about the orientational tissue structure inferred from diffusion MRI data to factor out the ‐direction dependence of the frequency difference signal.ResultsA human pilot study at 3 T demonstrates proxy maps of microscopic susceptibility anisotropy unconfounded by fiber crossings and orientation dispersion as well as magnetic field direction. The developed technique requires only a dual‐echo gradient‐echo scan acquired at 1 or 2 head orientations with respect to the magnetic field and a 2‐shell diffusion protocol achievable on standard scanners within practical scan times.ConclusionsThe quantitative recovery of microscopic susceptibility features in the presence of orientational heterogeneity potentially improves the assessment of microstructural tissue integrity.