Plastic waste increases at a rate of several tons per year and the time required for their biodegradation is often unknown. The Phanerochaete chysosporium fungus oxidizes a wide variety of toxic organic compounds to nontoxic compounds or CO2 and H2O. The biodegradability of the poly(vinyl alcohol) (PVOH) caused by this fungus was analyzed by gel permeation chromatography (GPC) with differential refractive index (Delta n) and ultraviolet (UV) detectors. During the GPC analyses, the PVOH is in contact with the components of the culture medium. These components can interact with the stationary phase and also with the polymer producing erroneous results in the molecular weight determination. Therefore, we compare results using different mobile phases. A phosphate-acetate buffer of pH 7.4 was found to be appropriate mobile phase to follow the degree of degradation of the PVOH by the change in the average molecular weight determined by GPC in this culture medium. UV detection enabled us to identify structural changes associated with transformations of the carbonyl groups, mainly to enolized beta-diketones groups. Infrared absorption (FTIR) confirmed these changes and also showed important modifications in the C-O stretching region probably due to apertures of cyclic ether groups or transformations of the OH groups by oxidation reactions.