Fourier Transform Infrared Attenuated Total Reflectance (FTIR-ATR) analyses of greige cotton fabrics bioscoured with a combination of ultrasound and endo- and exo-polygalacturonase enzymes obtained from Rhizopus sp. fungi were used in a fractional factorial design experiment to examine their performance. The statistical results indicate that endo- and exo-polygalacturonase enzyme treatments of greige cotton in combination with ultrasound are significantly different from control and could be an environmentally friendly alternative to the present-day caustic method for preparing cotton.