This study investigates the effectiveness of a same-day polymerase chain reaction (PCR) test for the rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) in a general screening of patients admitted to the trauma surgery and heart surgery department in a German university hospital. A total of 442 patients were screened over a 4-month period by using a PCR assay, compared to culture methods, for specimens from the nose and throat. The MRSA carriage rate on admission was 3.85% during the study period. The PCR results of 1,680 swabs showed a sensitivity of 85% and a specificity of 99.39% for swabs from the nares and for the throat 42.11% and 98.78%, respectively. A combination of specimens from the nose and throat from the same patient led to a sensitivity of 100% with a specificity of 98.29%. Cost calculation under the circumstances of a diagnosis-related groups (DRG) payment system found that the eight MRSA-positive patients created costs of 38,472 euros, i.e. 4,809 euros per patient, facing screening costs of 36.62 euros per sample. Screening patients by using the rapid PCR assay for a combination of specimens from the nose and throat would offer a safe and cost-effective way of MRSA screening on admission.