Low-energy electron-induced damage in hexadecanethiolate (HDT) monolayers on gold substrates has been investigated using infrared reflection-absorption spectroscopy (IRAS), angle-resolved near edge X-ray absorption fine structure spectroscopy (NEXAFS), and advancing water contact angle measurements. HDT films were exposed to electrons of energies 10-100 eV and doses between 30 and 14000 mu C/cm(2). The induced damage was monitored both "in situ" by NEXAFS measurements interleaved with electron irradiations and "ex-situ" by NEXAFS, IRAS, and contact angle measurements after exposure of the irradiated samples to air. A progressive film damage was observed with increasing electron energy and dose of irradiation. This damage was found to occur during irradiation in UHV and was not induced by chemical reactions with airborne molecules during subsequent exposure of the irradiated films to air. The damage starts in the region of the terminal methyl groups of the HDT films and propagates into the bulk of the film. An analysis of the IRAS and NEXAFS data shows that the conformational and orientational order within the HDT film are most sensitive to low-energy electron irradiation. Electron-induced cleavage of C-H and C-C bonds resulting in a partial desorption of the film constituents also occurs and leads to formation of C=C double bonds in the film as inferred from the appearance of a pi*-resonance in the C 1s NEXAFS spectra. The obtained results are of importance for both the optimization of self-assembled-monolayers-based lithography processes and for the general understanding of irradiation-induced changes in organic films.