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To test a multiplex real-time polymerase chain reaction (PCR) method for simultaneous detection of multiple organisms in bloodstream infections.Prospective observational study at the University of California Davis Medical Center (Sacramento, CA). Two hundred adult (>18 yrs) patients from the emergency room, intensive care units, and general medicine wards at risk of a bloodstream infection and who manifested signs of systemic inflammatory response syndrome (SIRS). Whole blood samples for PCR testing were collected at the same time as blood culture (BC). PCR results were compared to blood and other culture results.PCR detected potentially significant bacteria and fungi in 45 cases compared to 37 by BC. PCR detected the methicillin resistance (mecA) gene in all three culture-confirmed methicillin-resistant Staphylococcus aureus cases. More than 68% of PCR results were confirmed by blood, urine, and catheter culture. Independent clinical arbitrators could not rule out the potential clinical significance of organism(s) detected by PCR, but not by BC. PCR did not detect Enterococcus faecalis in five BC-confirmed cases. On average, seven patient samples could be tested simultaneously with the PCR method in 6.54 ± .27 hrs.Multiplex PCR detected potentially significant bacteria and fungi that were not found by BC. BC found organisms that were not detected by PCR. Despite limitations of both BC and PCR methods, PCR could serve as an adjunct to current culture methods to facilitate early detection of bloodstream infections. Early detection of microorganisms has the potential to facilitate evidence-based treatment decisions, antimicrobial selection, and adequacy of antimicrobial therapy.