Differently pre-treated cotton yarns were subjected to non-selective oxidation with perchloric acid and the effects of pretreatment processes on oxidation were studied through functional groups quantity, and degradation through mechanical properties and degree of polymerization. Different pre-treatments include, different scouring (with alkali, alkaline and acid pectinase), mercerization-different scouring as well as different scouring-mercerization. The quantity of functional groups was studied by measuring carboxyl groups with methylene blue and calcium-acetate methods and aldehyde groups with iodine and tetrazolium (TTC) methods. Pre-treatment processes affect the degree of elimination of non-cellulosic components of cotton and have strong influence on oxidation process. The non-selective oxidation of enzymatic scoured cotton with perchloric acid has introduced carboxyl and aldehyde groups without serious degradation of cotton yarns, confirmed by only 15 % decreasing of tensile strength and 8 % decreasing of degree of polymerization.