The atomic structure of YBa 2 Cu 3 O y fine crystalline HTSC samples with various average crystal lite sizes ranging from 0.4 to 2 μm and an oxygen concentration y close to the optimal value for super conductivity (y ≈ 6.93) is investigated by the neutron diffraction technique. We have found some effects asso ciated with the redistribution of cations and oxygen atoms and with variations in the positions of atomic layers in the unit cell, which are not observed in macrocrystalline samples. In all probability, these effects appear due to nonequilibrium conditions of synthesis required for obtaining this compound in the fine crystalline state. The results have made it possible to explain the peculiar physical properties of fine crystalline YBa 2 Cu 3 O y samples (in particular, the coexistence of high superconducting transition temperatures T c and noticeably lower values of magnetization in strong magnetic fields for T < T c ). It is shown that a nanoscale structural inhomogeneity exists in fine crystalline YBa 2 Cu 3 O y samples with the optimal oxygen content and changes the fundamental superconducting parameters, viz., the magnetic field penetration depth and the coherence length.