In order to determine the prevalence of S. aureus in clinical and subclinical bovine mastitis as well as the relationship between the presence of protein A gene and the udder inflammatory response .   A total of 400 quarter milk samples were collected from 100 lactating Friesian cows  at Ismailia Governorate . The percentage of clinical mastitis was   ( 19.5%.), while the percentage of subclinical mastitis according to C.M.T was ( 42.85%) . The percentage of  S.aureus   in clinical  mastitis was (28.2%) , while in  in subclinical mastitis  was (22.46% ).The identification of S,aureus was confirmed by PCR amplification of species-specific parts of the gene encoding the 16S rRNA. Twenty nine  S.aureus isolates were subjected to PCR for detection of X region of protein A (spA) gene,10 isolates from clinical mastitis and 19  isolates subclinical mastitiC milk specimens (+++ve CMT and ++ve CMT)  were (100%) positive . Results indicate that there  was a positive relationship between the  presence of protein A gene of S.aureus and the inflammation of udder in clinical mastitis as well as the high grades of subclinical mastitis.