The universal attenuated total reflectance Fourier transform infrared (UATR-FTIR) equipped with a ZnSe—Diamond composite crystal was used to analyze contaminated cotton fibers. Cotton samples were selected based on their high speed stickiness detector readings and sugar content as determined by high performance liquid chromatography. Trehalulose (dominant sugar in whitefly honeydew) was identified at 3280, 1622, and 1018 cm—1. Integrated intensities I3280, I1622, and I1018 showed high correlations with the trehalulose content on the contaminated lint. Principal component analysis of the FTIR spectra showed that it is possible to discriminate between contaminated and non-contaminated cotton and indicated that FTIR spectra of cotton lint fall into different clusters corresponding to different levels of contamination. The results obtained showed that the ZnSe—Diamond composite crystal FTIR accessory could be used as a fast and precise nondestructive method to discriminate between contaminated and non-contaminated cotton.