FT-Raman spectroscopy has been used to investigate treated verrucae (warts from the sole of the foot) with a local application of a salicylic acid paint. Differences in the molecular structure of the stratum corneum across the verruca sample were observed, and by comparison with normal and hyperkeratotic skin it was concluded that the tissue around the edges of the verrucae was typically hyperkeratotic skin. In the centre of the verruca, the molecular structure of the skin was altered showing evidence of the interaction with salicylic acid. Salicylic acid was not observed in its characteristic dimerised acid structure, but spectroscopic evidence suggested that fission of the intermolecular H-bonding essentially cleaved the dimer. Observed changes in the v(CCO) stretching mode of the carboxyl and hydroxyl groups indicate the inter H-bonds have broken. These spectral changes are believed to be more consistent with salicylic acid bonding within the human papillomavirus-containing verruca tissue rather than simple acid dissociation upon dissolution in water within the tissue. No evidence for the presence of the other paint components, lactic acid and flexible collodion, was found in the verrucae spectra. This Raman approach may help to elucidate the molecular basis for therapeutic agents interacting with diseased skin.