Microorganisms like bacteria, viruses, fungi, etc. have a major impact on human, animal, and plant life. Several decades ago it was observed that intact cells suspended in an isotonic salt solution moved toward the anode and the mobility was proportional to the density of the charge located on the cell surfaces. Since then, efforts have been made to make electrophoresis a useful tool in cell studies. Microorganisms are no exception. In the present work we applied the capillary zone electrophoresis (CZE) with dynamical modification of the capillary surface for separation of E. coli and P. vulgaris. The same method was used for identification of E. coli in infected urine (direct injection--UTIs) and also for identification of Helicobacter pylori which is a gram-negative bacillus responsible for one of the most common infections found in humans worldwide. Using spectrophotometric measurements at lambda = 214 nm we proved that it is possible to measure the concentration of bacterial cells up to 5 x 10(8) cells/mL. Recent studies have demonstrated very practical uses for electrophoretic techniques, especially in the field of medical diagnosis.