The layer-by-layer analysis of the rails classes such as the low-temperature reliability, increased wear resistance, and contact-fatigue strength rails of the superior category of quality after the bulk hardening and tempering and differentially hardening in different regimes is carried out by methods of transmission electron diffraction microscopy of thin foils in the layers located on the roller surface and at the distance of 2 and 10 mm from it on the central axis and on the round corner. The quantitative parameters of dislocation substructure, internal stress fields, structural and phase states formed by diffusion and shear mechanisms of $\gamma-\alpha$-transformation are established. The polycrystalline structure is formed in the surface layer of 10 mm thick, independently of the regime of hardening and rail category. The polycrystalline structure is presented by the pearlite grains of lamellar morphology, the ferrite grains, in the bulk of which one can observe the cementite particles of different shapes, and the grains of structurally free ferrite. The relative content of a given type of structure, depending on the hardening regime, rail category, and the depth of location of the layers, are studied. The main structural type of rail steel is pearlite of lamellar morphology with relative content changing in the range from 34% to 87%. Relative fraction of grains of ferrite–carbide mixture is slightly smaller (from 12% to 65% of steel structure). Relative volume fraction of grains of structurally free ferrite is small and is changed in the range from 1% to 5% of steel structure. Dispersion of pearlite structure is estimated, according to the value of interplate distance. As shown, the value of interplate distance is changed in the range from 105 nm to 200 nm. It depends on the regime of hardening, rail category, and distance to roller surface. The evaluation of rail strengthening mechanisms qualitatively being agreed with the hardness measurements is made. As established, the stress concentrator density reaches the maximum value at the tread contact surface. It is higher for the bulk-hardened rails than for differentially-hardened ones. As established, the ferrite component of steel structure is faulty. The dislocation substructures are revealed in the form of chaotically distributed dislocations, nets, cells, and fragments. In the ferrite of pearlite grains, only the first two types of dislocation substructure (namely, substructure of dislocation chaos and netlike dislocation substructure) are observed. The cellular and fragmentary dislocation substructures are revealed only in grains of structurally free ferrite and grains of ferrite–carbide mixture. Scalar dislocation density in ferrite component of rail structure under study is changed in the wide range from $2\cdot10^{10}$ cm$^2$ to $8\cdot10^{10}$ cm$^2$. By analysing the bend extinction contours, the sources of the internal-stress field concentrators are revealed. The most dangerous stress concentrators, which are predominantly formed in the rails subjected to the bulk hardening, are the ‘globular cementite particles–matrix’ interfaces.