Asymmetric flow field-flow fractionation (AsFlFFF) and high-performance size-exclusion chromatography (HPSEC) are techniques for separating and characterizing macromolecules; until now the latter is more utilized for analyzing polysaccharides. The demand for characterizing complex, high-molar-mass polysaccharides has raised interest in the use of AsFlFFF in analyzing polymeric carbohydrates in addition to HPSEC. In this paper, we compare the behavior of arabinoxylan aggregates present in aqueous solution in AsFlFFF and HPSEC and their effect on the obtained molecular characteristics (molar mass averages and size). Although the amount of aggregates in aqueous arabinoxylan solutions may be low, their role needs to be understood to avoid erroneous interpretations of AsFlFFF and HPSEC data. When these two separation systems were compared, AsFlFFF seemed to possess more separation power for the differentiation of aggregates from individual chains than HPSEC. To our knowledge, this is the first report on the characterization of xylans with AsFlFFF.