An investigation into the spectroscopic analysis of cotton waxes on Australian cottons was undertaken. The chemical composition of cotton wax is complex and contains a number of lipid classes. Infrared transmission spectroscopy coupled with principal component analysis was found to be capable of discriminating between solvent-extracted cotton waxes with differences in their alkyl functionality. Based on high-performance thin-layer chromatography (HPTLC) results, these differences were associated with an increase in levels of the alkane wax component. On the basis of these results, a photo-acoustic spectroscopic method was developed that could be used to distinguish raw cottons on the basis of these differences. This method was utilized to screen cottons from the Cotton Seed Distributors 2001 seed trial. A preliminary assessment of the scouring and dyeing properties of the various cottons, identified using the photo-acoustic method, was carried out. The results tended to confirm that cottons with increased alkyl functionality, most likely associated with alkane wax, were more difficult to remove and residual wax on the fiber acted as a barrier to dyestuff penetration, thus lowering color yield.