We report on the intrinsic crystalline structure of epitaxial ferroelectric Pb(Zr,Ti)O3 (PZT) films, which are fully relaxed from the stress of the substrate. The PZT films with the rhombohedral composition of Zr/Ti=68/32 were epitaxially grown on (001)Pt/(001)MgO substrates. Four-circle x-ray diffraction measurements revealed that the films showed not only perfect c-axis orientation, but also a tetragonal phase due to a clamping effect of the substrate. Successively, x-ray diffraction measurements using synchrotron radiation were carried out to examine the intrinsic structure of stress-free PZT films, which were powdered after substrate removal. The structure refinement by Rietveld analysis demonstrated that the films without substrates returned to a rhombohedral phase, however, 19% of the B site in the perovskite structure was occupied by Pb atoms. The phase-transition temperature from rhombohedral to cubic slightly decreased due to the anomalous structure of the stress-free PZT films. These results suggest that the deviation of the thin-film properties from the bulk ones is caused not only by in-plane epitaxial stress as an extrinsic factor, but also by the anomalous crystalline structure of the stress-free thin films.