A crude xylan isolate obtained by prehydrolysis and mild alkaline extraction from birch wood chips (Betula pendula), and a carefully delignified xylan fraction from the same source, were examined by dynamic light scattering (DLS) and cryogenic transmission electron microscopy (cryo-TEM) with regard to their propensity to self-assemble in water into insoluble aggregates. The delignification involved the extraction with chloroform of a crude xylan solution in a pyridine/acetic acid/water mixture. It resulted in a purified xylan fraction in a yield of 23% in which 75 and 90% of the lignin had been removed as indicated by Klason and UV-determination, respectively. It was found that both xylan fractions formed agglomerates by self-assembly in water. However, DLS and cryo-TEM indicated that the aggregates were larger in size (90 vs. 40 nm) and greater in mass when more lignin was present. The addition of an alkaline solution of isolated lignin (obtained by steam explosion) to increasing concentrations of a delignified xylan revealed increasing turbidity. Our conclusion is that lignin induces agglomeration of xylan in aqueous solutions, but xylan concentration plays an active role in the aggregation phenomena. An agglomeration mechanism for lignin rich xylan fractions is proposed.