A 4-O-methylglucuronoxylan was converted into a hexenuronoxylan at high temperature and alkalinity similar to the conditions used during kraft pulping. The hexenuronoxylan was hydrolysed with enzymes, and acidic xylooligosaccharides were separated from the hydrolysate by anion-exchange and size-exclusion chromatography. The primary structure of the two main hexenuronic acid-substituted xylooligosaccharides (a tetramer and a pentamer) was determined by two-dimensional 1H and 13C NMR spectroscopy. The 4-deoxy-hexenutronic acid is not stable under the acid hydrolysis step of conventional carbohydrate analysis. Here, we have identified the acidic degradation products of 4-deoxy-hexenuronic acid by NMR spectroscopy. Two degradation pathways were observed, both resulting in a furan derivative.