The IDI-MRSA assay (Infectio Diagnostic, Inc., Sainte-Foy, Quebec, Canada) with the Smart Cycler II rapid DNA amplification system (Cepheid, Sunnyvale, CA) appears to be sensitive and specific for the rapid detection of nasal colonization by methicillin-resistant Staphylococcus aureus (MRSA). We assessed the sensitivity and specificity of this assay under conditions in which both the nose and cutaneous groin specimens were analyzed together and compared the accuracy of this PCR approach to that when these specimens were tested separately and by culture assays in an inpatient population with known high rates (12 to 15%) of MRSA colonization. Of 211 patients screened, 192 had results assessable by all three methods (agar-broth culture, separate nose and groin IDI-MRSA assay, and combined nose-groin IDI-MRSA assay), with MRSA carriage noted in 31/192 (16.1%), 41/192 (21.4%), and 36/192 (18.8%) patients by each method, respectively. Compared to agar culture results, the sensitivity and specificity of the combined nose-groin IDI-MRSA assay were 88.0% and 91.6%, respectively, whereas when each specimen was processed separately, the sensitivities were 90.0% (nose) and 83.3% (groin) and the specificities were 91.7% (nose) and 90.2% (groin). IDI-MRSA assay of a combined nose-groin specimen appears to have an accuracy similar to that of the current recommended PCR protocol, providing results in a clinically useful time frame, and may represent a more cost-effective approach to using this assay for screening for MRSA colonization.