Three-dimensional documentation of the axonal pathways connecting gray matter components of the human brain has wide-ranging scientific and clinical applications. Recent attempts to map human structural connectomes have concentrated on using tractography results derived from diffusion-weighted imaging data, but tractography is an indirect method with numerous limitations. Advances in holographic visualization platforms provide a new medium to integrate anatomical data, as well as a novel working environment for collaborative interaction between neuroanatomists and brain-imaging scientists. Therefore, we developed the first holographic interface for building axonal pathways, populated it with human histological and structural MRI data, and assembled world expert neuroanatomists to interactively define axonal trajectories of the cortical, basal ganglia, and cerebellar systems. This blending of advanced visualization hardware, software development, and neuroanatomy data enabled the translation of decades of amassed knowledge into a human axonal pathway atlas that can be applied to educational, scientific, or clinical investigations.