Ion-pair formation of polyammonium ions with aromatic disulfonates (ADSs) has been investigated with ion-exchange chromatography. Data obtained imply that polyethyleneammonium ions [NH(3)(+)(CH(2)CH(2)NH(2)(+))(n)H] recognize the lengths between sulfonate groups in ADSs in the absence of specific ion-pair formation. The molecular length of the diethylenetriammonium ion is almost equal to that between sulfonate groups in ADSs tested when this polyammonium ion adopts an all-trans conformation; the match of lengths dominates ion-pair formation. However, anthraquinone-1,8-disulfonate (1,8-AnDS) shows a different behavior. This compound specifically interacts with polyammonium ions having an ethylenediammonium structure in a molecular terminal and forms much more stable ion-pairs than any other ADS. It is speculated that the accommodation of a terminal ammonium ion in the pocket consisting of two sulfonate groups in the 1,8-AnDS molecule allows stable complex formation. These are applied to the enhancement of the selectivity in chromatographic and electrophoretic separation of ADS.