Fourier transform infrared (FTIR) spectroscopy in the attenuated total reflectance mode (ATR) was used to characterise SiOxHy thin films deposited on either polypropylene foil or silicon wafers through a cold atmospheric plasma discharge. Compared to a classical transmission spectrum with transverse (TO) vibrational modes, the FTIR-ATR spectra revealed modified and/or exhibited additional features caused by either the non-orthogonal angle of incidence of the infrared radiation with respect to the sample normal or the partial light reflection on the deposition substrate. On one hand, recording the infrared spectra with an angle of incidence other than 90 degrees produced a longitudinal (perpendicular to the sample normal) component in the electric field of the incident light, which enabled the detection of longitudinal (LO) vibrational modes. On the other hand, the transverse vibrational modes of thin films deposited on silicon were slightly extinguished with a concomitant increase of the spectral intensity of the LO features, due to both the partial withdrawing between the incident and reflected electric fields of the infrared light lying in the sample plane and, the addition of those perpendicular to this sample plane. These data thus clearly show the enormous potential of FTIR-ATR to characterise thin film molecular order, provided that a prior comprehensive analysis is performed on the sampling depth and the light reflection on the deposition substrate. (C) 2013 Elsevier B.V. All rights reserved.