Diagnostic microbiology laboratories and reference laboratories are key for identifying outbreaks of MRSA. New rapid techniques for the identification and characterization of MRSA have been developed. This notwithstanding, the bacterium generally must be cultured via blood, urine, sputum, or other body fluid cultures, and grown up in the lab in sufficient numbers to perform these confimatory tests first, so there is no quick and easy method to diagnose an MRSA infection, therefore initial treatment is often based upon 'strong suspicion' by the treating physician, since any delay in treating this type of infection can have fatal consequences. These techniques include Real-time PCR and Quantitative PCR and are increasingly being employed in clinical laboratories for the rapid detection and identification of MRSA strains.

Another common laboratory test is a rapid latex agglutination test that detects the PBP2a protein. PBP2a is a variant penicillin-binding protein that imparts the ability of S. aureus to be resistant to oxacillin.