The aim of the present study was to determine the diagnostic value of a single-locus real-time polymerase chain reaction (PCR) recently proposed for rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) from clinical samples (IDI-MRSA; Infectio Diagnostic, Sainte-Foy, Québec, Canada). This test, which was developed on the basis of studies of the sequence analysis of the mecA gene carried by staphylococcal cassette chromosome mec (SCCmec), was used to screen nasal swabs of 320 intensive care unit (ICU) patients at admission. The results were compared with those of conventional culture of swabs from several body sites. When compared with culture of swabs from the nose, throat, and wounds, the diagnostic values of the real-time PCR test from nasal swabs were as follows: 92.3% sensitivity, 98.6% specificity, 75.0% positive predictive value, and 99.6% negative predictive value. Fifteen (4.7%) samples could not be evaluated because the PCR reaction was inhibited, even after the samples were frozen and thawed for retesting. Culture of nasal swabs showed that 78 of the patients were colonized with methicillin-susceptible S. aureus. Unexpectedly, 4 (5.1%) of these samples gave false-positive results in the IDI-MRSA. These isolates were all single clones, as shown by pulsed-field gel electrophoresis and spa typing. Reliable results were obtained with the IDI-MRSA assay, even in a patient population with a low prevalence (approximately 4%) of MRSA and even when compared with swabs of different body sites. Nevertheless, further work is needed to reduce the inhibition rate of the PCR and to explain why false-positive results were obtained with methicillin-susceptible S. aureus.