The ability of tetraalkylammonium salts to act as ion-pairing agents for betacyanins and mono- as well as bidecarboxylated betacyanins in HPLC on reversed phase is reported. The results indicate substantial and various influences of tetraalkylammonium salt addition to eluent on magnitude and direction of retention time changes of the analytes. The interactions of the tetraalkylammonium cations with the accessible positive and negative charged parts of the analysed molecules at their different level and position of decarboxylation determined the possibility of ion-pair formation. A remarkable positive influence was observed for betacyanins on the basis of strongly enhanced retention of the resulted ion-pairs. In contrast, the 2,17-bidecarboxy-betacyanin retention, in most of the applied conditions, strongly decreased under the impact of the reagents. The effect of the salt concentration on direction of 17-decarboxy-betacyanin and 2,17-bidecarboxy-betacyanin retention changes strongly varied with the eluent pH. The carboxylic group at the C-2 carbon cannot interact with tetraalkylammonium cations as strongly as does the C-17 carboxylic group, leading to different effects in the absence of carboxylic group at the C-2 or C-17 carbon in the molecules.