Fourier transform infrared (FTIR) microspectroscopy has been employed to investigate benign (ordinary dermal and Reed nevi), dysplastic and malignant (invasive melanoma) skin lesions through the analysis of spectral changes of melanocytes as well as in the evaluation of the presence of melanin. Hierarchical cluster analysis and principal component analysis led to a satisfactory separation of malignant from dysplastic and normal melanocytes. Also, on enlarging the clustering with spectra from Reed and dermal nevi, the multivariate analysis segregated well the spectral data into discrete clusters, allowing the obtaining of reliable average spectra for analysis at the molecular level of the main groups or components responsible for the biological and biochemical changes. The most significant spectral characteristics appear to be related to differences in secondary protein structures, in nucleic acid conformation, in intra- and intermolecular bonding. In all cases, supervised and unsupervised spectral analyses resulted in satisfactory agreement with histopathological findings.