Electrophoretic behavior and pK a determination of six quinolones with a piperazinyl substituent, together with two quinolones without a piperazinyl substituent and 1-phenylpiperazine, were investigated by capillary zone electrophoresis. The results indicate that quinolones with a piperazinyl substituent involve three protonation/deprotonation equilibria. The results also suggest that the contribution of the zwitterionic species of these quinolones to the effective mobility may not be neglected. This is probably due to a slightly incomplete protonation of the piperazinyl moiety in the pH range of 6.0–8.0, compared with the complete dissociation of the carboxylic group. Consequently, the zwitterionic species of ciprofloxacin, in particular, is slightly negatively charged. With the aid of computer simulation, three pK a values were determined for quinolones with a piperazinyl substituent, thus allowing us to rationalize precisely the influence of pH on the electrophoretic behavior of these compounds.