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Human hair, like other Alpha-keratinous fibres, is a highly complex biomaterial. The application of analytical methods to human hair is used in the assessment of chemical damage, constituting the first step to prevent hair deterioration and to develop new products; making hair analysis a very important method for the cosmetic industry and hair researchers. Very little systematic research on the protein patterns of the keratin structures of human hair and how they relate to chemical damage have been reported. This study set out to develop advance techniques which are only rarely used on keratin fibres, where it focuses on gel electrophoresis. The study aims to standardise the data acquisition process, also refining the data analysis methodology for extracting more in-depth information at the molecular level. The techniques included two different types of electrophoresis (SDS-PAGE and the PhastSystem), differential scanning calorimetry (DSC), attenuated fourier transmission spectroscopy (ATR-FTIR) and transmission-FTIR. By suggesting the extraction, staining and destaining times allows to minimise the measurement variability in the protein patterns, thus allowing for more repeatable protein pattern analysis with less sample-to-sample variation. Methods for both the standardisation length of the protein patterns and using the normalisation of the intensity variations have been proposed and this approach has not been attempted before. In human hair the clustering method, demonstrates high correlation between populations of human hair samples. The content of the amino acids, cysteine and cysteic acid, show in the case of darker hair colour a systematic increase, confirmed by use of transmission-FTIR along with ATR-FTIR. A significant increase in extractability is accompanied with an increase in cysteic acid content in cuticle, as presented by dark shade sample with high extractability. For animal hair, the chemical damage in the keratin intermediate filament proteins (KIFs) or keratin intermediate filament-associated proteins (KAPs) levels was analysed and cluster analysis was proposed as a way to classify animal hair fibres by sub species. The application and optimisation of the electrophoresis analytical methods to human and animal hair in the assessment of chemical damage is novel and very useful for the cosmetic industry, hair researchers and related forensic applications. A further investigation using transmission FTIR could be used in the analysis of the amount of cysteic acid in the cortex could be carried out similar to that which was carried out for the cuticle.