We have studied the effect of He+ irradiation with doses in the range 1012–2×1015 cm−2 on two high-temperature superconducting structures: YBa2Cu3O7−x (YBCO) films and YBa2Cu3O7−x/PrBa2Cu3O7 (YBCO/PBCO) superlattices. In particular we have focused on superlattices [YBCON/PBCOM]1000 Å with N=1, 8 unit cells of YBCO, and M=5 unit cells of PBCO, with a total thickness of 1000 Å. The analysis is presented in terms of depression of the critical temperature (Tc) and modification of the crystalline structure using X ray refinement technique. Single films show a systematic increase in the c-lattice parameter upon irradiation, which is not observed in thin one unit cell YBCO layers in superlattice structures. However, Tc depression resulting from irradiation is deeper in superlattices. These results are explained considering the strained nature of the as-grown [YBCON/PBCO5]1000 Å superlattices with low values of N. Both structures show persistent photoconductivity, indicating that defects are related to oxygen displacements in the Cu–O chains.