Selective, high-efficiency separations of intact bacteria may, in some cases, allow them to be identified and quantified in much the same way that molecules are done today. Two different capillary electrokinetic approaches were utilized. The first approach used a dissolved polymer-based CE separation that may be affected by size and shape considerations. Another approach uses capillary isoelectric focusing to separate bacteria by their surface charge or isoelectric point. Good peak shapes and extremely high efficiencies are observed (up to ~ 1 600 000 theoretical plates/m). Careful sample preparation and separation runs are essential in order to obtain reproducible separations. Expansion of these types of rapid, efficient microbial separations could have profound effects on many branches of science and technology.