A new polarization–interference biomedical diagnostic three-dimensional (3D) Jones-matrix technology with digital Fourier reconstruction of layered maps of optical anisotropy (thesiograms) of dehydrated films (facies) of biological fluids of human organs is presented and experimentally tested. An original model of layered phase scanning of polycrystalline architectonics of supramolecular networks of biological fluid facies is proposed for the purpose of theoretical justification and prognostic use of the obtained results. On its basis, algorithms of Jones-matrix reconstruction of thesiograms of birefringence and dichroism of facies of synovial fluid, bile and blood are found. As a result, layered thesiograms of linear and circular birefringence and dichroism of facies with different spatial–angular architectonics of supramolecular networks are experimentally obtained for the first time. Within the framework of statistical analysis of experimental data, new objective markers (asymmetry and excess of optical anisotropy parameter distributions) for diagnostics of pathological changes in the optical anisotropy of biological fluid facies were defined and clinically tested. As a result, an excellent level of balanced accuracy of the developed polarization–interference Jones-matrix method of layer-by-layer reconstruction of thesiograms of polycrystalline supramolecular networks in differential diagnostics of bile facies (cholelithiasis), synovial fluid (reactive synovitis–septic arthritis) and whole blood (follicular adenoma–papillary thyroid cancer) was achieved.