Five amphoteric piperazinyl fluoroquinolones, which are bases in acidic conditions, and flumequine, which is neutral at a low pH, were analyzed in a RP system on cyano-silica plates with acetonitrile/aqueous acidic mobile phases containing various concentrations of potassium perchlorate. Perchlorate, which is so-called chaotropic ion, was supposed to cause the increase in the retention of basic fluoroquinolones. Unexpectedly, the retention of the drugs decreased with increasing concentrations of perchlorate anion, which was the most evident for the plates pre-washed before use with an ACN/H2O (60:40) mixture. Retention of flumequine seemed to be independent from the chaotropic ion concentration.