In this pilot study, we have demonstrated the utility of capillary zone electrophoresis as a fast and low-cost method to detect serious bloodstream infection caused by MRSA strains. The blood-incubated methicillin-resistant and methicillin-susceptible S. aureus strains were differentiated from each other by CZE on GOTMS-modified FS capillaries etched with supercritical water. The number of injected purified cells was sufficient for rapid screening of clinical samples. A minimum of two hundred MRSA cells from 2 mL of whole human blood were detected but the RSDs varied between 7 and 40% for the peak areas. This qualitative value provides sufficient information for the initiation of effective antibiotic therapy. Specifically, the purification procedure should be improved. If the purification procedure is more efficient, we will be able to analyze a lower number of cells. That will be interesting for clinical practice. The CZE also allows discrimination between the MH agar-cultivated and the blood-incubated MRSA or MSSA cells due to their different surface properties. The isoelectric point of both MH agar-cultivated and blood-incubated cell has not changed.