Given the worldwide production, usage, and manufacturing of cotton, protocols that could identify botanical cotton trash components that can become comingled with cotton could be advantageous for quality assessment prior to spinning. Conventional methods such as the High Volume Instrument (HVITM) or Shirley Analyzer do not classify or yield specific trash component information. A program was implemented 1) to determine the efficacy of the ultraviolet-visible (UV-Vis) spectroscopy technique to identify cotton trash types and 2) to compare these identification results to the results of the Fourier-transform near-infrared (FT-NIR) technique to identify cotton and individual cotton trash components. Chemometric routines involve preprocessing methods and evaluation of specific spectral wavelengths to enhance spectral differences among individual pure samples of cotton trash components and cotton fiber. The chemometric software package, Unscrambler, afforded a 67% correct botanical trash identification. The utility of this method to correctly identify cotton fiber and cotton trash components was compared to the FT-NIR spectrometer. Overall, a higher percentage of correct identifications (98%) were observed using the FT-NIR spectrometer coupled with the OPUS IDENT software package. When comparing OPUS IDENT and Unscrambler software packages for sample identification by uploading NIR data into Unscrambler, the FT-NIR identification results with Unscrambler were significantly superior to the UV-Vis identification results. Thus, the FT-NIR technique proved to be a better technique than the UV-Vis technique at identifying cotton trash types.