Staphylococcus aureus is a common cause of infection in both hospitals and the community, and it is becoming increasingly virulent and resistant to antibiotics. Possibilities of fast, sensitive and cheap determination of these pathogenic bacteria are extremely important in antimicrobial therapy. In the present study, CE with chemically modified capillary and zeta potential measurements were used for differentiation of three different clinical strains of S. aureus. The data presented in this contribution suggested that electrophoretic behavior and the values of zeta potential should be very useful in distinguishing between closely related strains, which exhibited coagulase gene/protein polymorphism. Understanding the differences between S. aureus strains could help to improve our knowledge about S. aureus pathogenecity and to monitor for and respond to emergence of more virulent strains.