Staphylococcus aureus is a relatively clonal microorganism that causes subclinical and clinical mastitis. Cases of mastitis in cows at Baturraden are leading to signifi cant and ongoing problems due to reduced production and lower milk quality. This study was designed to identify which of selected virulence determinant genes of S. aureus are involved in the Baturraden infection, and to determine the clonal relationship among these isolates. Seventeen isolates were identifi ed as S. aureus based on their biochemical properties and species specifi city for 23S rRNA and nuc genes. S. aureus isolates were genotypically characterized for the selected virulence determinants: coa, clfA, fnbA, fnbB, cap5, spa IgG and spa X-region genes. Clonal relationship analysis among isolates was carried out using AFLP and results compared with previously confi rmed relationships between selected S. aureus isolated from other regions. The results show that eight isolates contain all the genes, but six isolates lack fnbB and two isolates lack cap5 genes. AFLP analysis showed that all isolates of S. aureus originating from cows in Baturraden belong to one cluster. This study provides additional knowledge about S. aureus infection in Baturraden cows, including the number of virulence determinant genes that may play a role in pathogenicity.