Staphylococcus aureus is a common cause of bovine mastitis that is responsible for the main economic loss to the dairy industry. For identification of putative, bovine-specific molecular marker a genome comparison between bovine S. aureus strain RF122 and 52 previously sequenced S. aureus isolates associated with human infections using genome viewer, annotation tool Artemis Comparison Tool (ACT), KEGG and NCBI BLAST databases was carried out. This led to the identification of 16 unique RF122 gene sequences that may be used as molecular marker to distinguish bovine from human strains. The distribution of these genes was analyzed in a collection of bovine mastitis strains from the Netherlands and human clinical isolates by PCR and Southern blotting. Only four genes within the pathogenicity island SaPIbov3 (sab 1890, sab1891, sob 1892, sab1893) were present in the majority of isolates from cattle but were absent from human clinical S. aureus isolates. These results suggest that there is no gene/ORF uniformly shared by all bovine S. aureus strains that could be uniformly used as a diagnostic marker gene. (C) 2010 Elsevier B.V. All rights reserved.