Plasma polymerization is traditionally recognized as a homogeneous film-forming technique. It is nevertheless reasonable to ask whether micrometer thick plasma polymerized structures are really homogeneous across the film thickness. Studying the properties of the interfacial, near-the-substrate (NTS) region in plasma polymer films represents particular experimental challenges due to the inaccessibility of the buried layers. In this investigation, a novel non-destructive approach has been utilized to evaluate the homogeneity of plasma polymerized acrylic acid (PPAc) and 1,7-octadiene (PPOD) films in a single measurement. Studying the variations of refractive index throughout the depth of the films was facilitated by a home-built surface plasmon resonance (SPR)/optical waveguide (OWG) spectroscopy setup. It has been shown that the NTS layer of both PPAc and PPOD films exhibits a significantly lower refractive index than the bulk of the film that is believed to indicate a higher concentration of internal voids. Our results provide new insights into the growth mechanisms of plasma polymer films and challenge the traditional view that considers plasma polymers as homogeneous and continuous structures.