Staphylococcus aureus is one of the most widespread mastitis pathogens infecting dairy cattle worldwide. In Switzerland, different bovine genotypes of Staph. aureus have been identified, and genotype B (GTB) was demonstrated to be a highly contagious subtype, causing herd problems in cattle. As the efficacy of antibiotic therapy against Staph. aureus is not satisfactory, the most promising strategy for controlling this udder pathogen is the implementation of specific sanitation programs for affected farms. The aim of the present longitudinal study was the field evaluation of 2 analytical approaches for the sanitation of Staph. aureus GTBpositive dairy herds. We compared a new real-time quantitative PCR (qPCR) assay based on the detection of the unique target gene adlb with classical bacteriology. Sanitation was successfully achieved using both analytical methods, but the qPCR approach showed some main advantages, namely the use of clean (instead of aseptically collected) milk samples facilitates sample collection in terms of time and costs, enabling the sampling of entire herds during a regular milking procedure and by the farm staff. The high inclusivity and exclusivity of the new target gene adlb enable very specific detection of only the genotype of interest. Because of the very high diagnostic sensitivity of qPCR, each GTB-positive cow can be correctly identified at any time point during lactation, allowing farmers to continuously update milking groups to prevent transmission during milking. Milk sample analysis becomes more objective, faster, less expensive, and more suitable for routine application, enabling the sanitation of even big herds in short time.