Recent developments of methods for mapping tissue microstructure with MRI require histological 3D data for validation. Here, CLARITY on post mortem human brain was adapted for this purpose. We demonstrated clearing of up to 8 mm thick samples, 3D microscopy of up to 5 mm thick samples, and the application of multiple stains including markers for neurons, glia, and fibers. The result is a detailed histology-based characterization of cyto- and myelo-architectonics within a volume corresponding to a typical MRI voxel. This approach promises to help integrate MRI-based histology and optical microscopy in 3D, and enable the further development and validation of in vivo histology using MRI.