Bacteria, bacterial metabolites and cell components can have a positive as well as negative impact on human health. Therefore, there is a strong need for determination of bacteria and bacterial metabolites in various samples, including food, natural objects, and biological fluids. Capillary electrophoresis (CE) is a powerful tool for the identification and separation of ionic compounds, characterized by high efficiency, low background electrolyte consumption, low sample volume and simplified sample preparation. Here we review recent applications of electrokinetic methods in combination with various detection systems and on-line concentration techniques for the analysis of bacterial metabolites, cell components, and bacteria. The modification of electrophoretic systems aiming to achieve superior analytes resolution and application of bacteria as a modifier of both background electrolyte and capillary walls are discussed. Therefore, this review provides a thorough analysis of applications and offers practical recommendations on the CE implementation for the bacterial samples.