The molecular structure of poly[biphenyl dianhydride-p-phenylenediamine] (BPDA-PDA) polyimide in ultrathin (3-300 nm) films on silicon has been characterized by polarized infrared spectroscopy in conjunction with ellipsometry and X-ray reflectivity measurements. In spite of the high degree of crystalline packing of the polymer chains, the results show that an unexpected and significant content of imide rings exhibit local structural perturbations, including out-of-plane twisting. Further, the fraction of perturbed rings increases with increasing film thickness while, in contrast, the high degree of in-plane uniaxial film symmetry and planar stacking of the chains remain constant with thickness. These results reveal a new structural aspect of localized ring disorder that arises within the otherwise well-ordered, chain-stacked structure of BPDA-PDA polyimide films.