Abstract The degradation of chitosan by hydrogen peroxide was studied. The degradation was monitored by gel permeation chromatography (GPC). The molecular weight distribution of partially degraded products from homogeneous reaction displayed a single-modal curve whereas that from heterogeneous reaction was bimodal. The molecular weight (Mw) decreased as the temperature, the time and/or hydrogen peroxide concentration increased. The dissolution of chitosan (pH 5.5) in minimum hydrochloride enhanced its degradation, but excessive hydrogen ion potentially inhibited the degradation. The formation of carboxyl group and deamination in the products indicated that the decrease of Mw was accompanied by structure changes. The degraded chitosans in Mw range from 51×10 3 to 1.2×10 3 were characterized by elemental analysis, X-ray diffraction, thermogravimetric analysis (TGA) and differential thermal analysis (DTA), Fourier transform infrared (FT–IR), carbon-13 nuclear magnetic resonance spectroscopy ( 13C-NMR). There was no significant chemical change in the backbone of chitosan with Mw of 51×10 3. But degraded chitosan with Mw of 3.5×10 3 had 1.71 mmol/g carboxyl groups and lost about 15% of amino groups. Further degradation led to more ring-opening oxidation of degraded products, the formation of carboxyl groups and faster deamination. The degraded chitosan with Mw of 1.2×10 3 had 2.86 mmol/g carboxyl groups and lost more than 40% of amino groups.