We have studied the effect of thickness on the structure and superconductivity of Nd 1.2Ba 1.8Cu 3O 7+ x (NdBCO) epitaxial films deposited on SrTiO 3 (1 0 0) substrates. High quality NdBCO films were deposited by high oxygen pressure sputtering. The samples have been carefully characterized by transport measurements and X-ray diffraction using conventional and synchrotron radiation sources. Two structural transformations are observed. The first one is a crossover from the orthorhombic and twinned structure, typical of thick samples, to a pseudotetragonal phase at thickness lower than 60 unit cells. The pseudotetragonal phase exhibits peculiar X-ray diffuse scattering around the Bragg reflections, associated to nanostructured twinned domains. The second one appears at thickness lower than 20 unit cells and is assigned to a pseudotetragonal–tetragonal transition. The transport properties are not modified at the first crossover, while a substantial decrease of T c and of the number of holes is observed at the pseudotetragonal–tetragonal transformation. Our results suggest that the structural rearrangement and the transport properties are explained by the ordering of Cu(1)O chains.