Polyelectrolyte multilayers (PEMs) produced by layer-by-layer (LbL) self-assembly find different applications. Often the PEMs are exposed to mechanical stress which they have to sustain. A correlation of the mechanical properties of PEM on macroscopic level with the ordering of polyelectrolyte molecules on molecular level is of interest. Our study is focused on the changes of orientation of the polyelectrolyte molecules when the PEM is under lateral mechanical stress. The PEM was prepared from pyrene (PY) labeled polystyrene sulfonate (PSS-PY) and poly(diallyldimethylammonium) chloride (PDDA) on sheets of polydimethylsiloxane (PDMS) rubber used as substrates. The LbL dipping technique was used for the formation of PEMs. A special stretching device was constructed which allows the fluorescence of the films under stress to be observed. The change in the fluorescence spectra which can be attributed to a PY ordering change from the PEM under stress of up to 10% was monitored. We observed that PEMs undergo a plastic deformation under external mechanical stretching. We conclude that under mechanical stress the polyelectrolyte molecules organized in polyelectrolyte multilayers experience an irreversible transition from the coiled to decoded state.