Active surveillance for meticillin-resistant Staphylococcus aureus (MRSA) carriers is considered an essential component of MRSA control strategies in acute care hospitals. Recently, molecular assays for MRSA screening have been proposed with significant reduction of the sample processing time. Using a time analysis model, we investigated the time gain after the introduction of a molecular assay and compared this with a preceding control period, using culture-based techniques. During a four-month period all high risk patients (N=44) and all known MRSA-positive patients readmitted to the hospital (N=41) were screened for MRSA upon admission. In both groups the long pre-analytical phase – time from admission to sampling and transportation of samples to the laboratory – was the determining factor in the entire process. A substantial reduction of the sample processing time was achieved using molecular assays, compared with conventional culture. Due to the long pre-analytical phase, in addition to the high costs associated with polymerase chain reaction (PCR) testing, molecular techniques were not introduced for the admission screenings. In the group of the readmission screenings, however, a fast test result could save a substantial number of unnecessary isolation days, resulting in an economic benefit for the hospital. PCR testing might be of interest for the readmission screenings. In conclusion, local policies for MRSA screening should be investigated before introducing expensive PCR technology.