The importance of electromigration techniques in molecular biology and medicine is increasing rapidly, especially in systematic studies on proteomes and metabolomes. Staphylococcus aureus and Escherichia coli are bacterial species most frequently encountered in human infections, and many serious illnesses can be observed in the hospital environment. In this contribution we proposed a CE method with different modification of internal capillary surface and with monolithic beds as a selective material for determination of bacteria in clinical samples. The electrophoretic separation depends on the differential mobility of bacteria in the capillary and selective interactions between bacterial cells and stationary phases (modified surface, monolithic beads). Proposed procedures could become an effective tool for diagnosis of certain diseases caused by S. aureus and E. coli as well as Proteus vulgaris.