The microwave properties and the crystal structure of YBa2Cu3O7−&dgr;thin films are examined as a function of film thickness. Already below the critical thickness for the formation of macroscopic fractures, we observe an increase of the residual surface resistance with thickness. Cross‐sectional transmission electron microscopy reveals that this behavior is caused by structural changes of antiphase boundaries leading to normal‐conducting regions between superconducting grains. The surface resistance is calculated within the weak‐link picture. ©1996 American Institute of Physics.