Heteroxylans (HX) from vitreous and floury parts of maize endosperm were isolated. Structural analysis showed a xylan backbone with few unsubstituted xylose residues (<9%) demonstrating the high content in side chains in both fractions. HX from floury endosperm contained more arabinose and galactose than vitreous HX. The mono-substitution rate was 15% higher in the vitreous endosperm HX. Similar amounts of uronic acids were present in both fractions (~7% DM). Galactose in the floury endosperm HX was present exclusively in terminal position. A xylanase preparation solubilized more material from floury (40.5%) than from vitreous endosperm cell walls (15%). This could be a consequence of the structural differences between the two fractions and/or of the impact of structure on the interaction abilities of these fractions with other cell wall polysaccharides. Our study advances the understanding of cell wall polysaccharides in maize endosperm and their role in enzymatic susceptibility of maize grain. •Heteroxylans (HX) from vitreous and floury endosperm of maize were characterized.•The floury endosperm contains more cell wall components than the vitreous one.•Vitreous HX contains 15% more mono-substituted xylose than floury HX.•Xylanases solubilized ~2.5 more matter from floury than from vitreous cell walls.•The results will allow improving the enzymatic preparations used in animal feeding.