Chitosan was depolymerized either by HCl hydrolysis or enzymatic degradation with a commercial preparation Pectinex Ultra Spl. The chitooligosaccharides released by both methods were selectively precipitated in methanol solutions and characterized using MALDI-TOF mass spectrometry. Differences between the two methods were detected and concerned the degrees of polymerization of the fragments produced and their acetylation. The enzymatic method yielded shorter fragments with a higher proportion of fully deacetylated chitooligomers. Conversely, acid hydrolysis of the starting chitosan resulted in fragments with degrees of polymerization up to sixteen and more monoacetylated residues than with the enzymatic procedure.