It has been shown that diverse strains of bacteria can be separated according to their characteristic surface properties by means of CE. We employed here this analytical technique to the study of colistin-resistance in Gram-negative bacteria, which involves the selection of mutants with modified outer membrane composition resulting in changes of surface cell properties. In the same way as with molecular entities, we performed firstly the validation of an ITP-based CE method for three common pathogenic Gram-negative bacteria namely Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Secondly, we compared the electrophoretic profiles of bacterial samples from a colistin-susceptible clinical isolate of K. pneumoniae and from the corresponding colistin-resistant derivative. By a simple CE run taking a few minutes, the coexistence of several bacterial subpopulations in the colistin-resistant derivative was clearly evidenced. This work encourages further research that would allow applications of CE in clinical laboratory for a daily monitoring of bacterial population in cared patients when "last-chance" colistin treatment is initiated against multidrug-resistant bacteria.