The effect of ethanol extraction on plasma-polymerized allylamine ( PPAA) films was investigated by measuring their thickness change using surface plasmon resonance ( SPR) spectroscopy and optical waveguide spectroscopy ( OWS). It was found that much of the freshly deposited PPAA films is lost upon ethanol treatment. The decrease in PPAA thickness is related to the plasma input power, the monomer vapor pressure, and the thickness of the deposited films. Despite the relatively high loss in film thickness, the densities of the amine groups in the extracted PPAA are comparable to those of fresh films, as seen by Fourier transform infrared ( FT-IR) spectroscopy. The results of this study are of specific importance with respect to the biomedical application of plasma-polymerized functional thin films, in which the stability of a plasma polymer in contact with aqueous media is essential.