Domains of remnant polarization can be written into ferroelectrics with nanoscale precision using scanning probe nanolithography techniques such as piezoresponse force microscopy (PFM). Understanding the structural effects accompanying this process has been challenging due to the lack of appropriate structural characterization tools. Synchrotron X-ray nanodiffraction provides images of the domain structure written by PFM into an epitaxial Pb(Zr,Ti)O(3) thin film and simultaneously reveals structural effects arising from the writing process. A coherent scattering simulation including the superposition of the beams simultaneously diffracted by multiple mosaic blocks provides an excellent fit to the observed diffraction patterns. Domains in which the polarization is reversed from the as-grown state have a strain of up to 0.1% representing the piezoelectric response to unscreened surface charges. An additional X-ray microdiffraction study of the photon-energy dependence of the difference in diffracted intensity between opposite polarization states shows that this contrast has a crystallographic origin. The sign and magnitude of the intensity contrast between domains of opposite polarization are consistent with the polarization expected from PFM images and with the writing of domains through the entire thickness of the ferroelectric layer. The strain induced by writing provides a significant additional contribution to the increased free energy of the written domain state with respect to a uniformly polarized state.