At present, detection and identification of microorganisms in real biological samples needs very sensitive methods for correct diagnosis and therapy in medical practice, biotechnology, agriculture, food safety and quality etc. Accordingly, it is essential to develop new cheap techniques for pathogen identification, particularly for pathogen in complex biological samples. Pre-concentration, separation, and sensitive detection of whole cells in one step are great potential and advantage for detection of pathogens in low concentration. Combination of filtration microcartridge and capillary isoelectric focusing was developed for pre-concentration and pre-separation of microorganisms from real suspensions and the possibility its application to real samples was verified.