This study was conducted to investigate the antimicrobial susceptibility, Panton Valentine leucocidine (PVL) and toxin (enterotoxin A-J, staphylococcal toxic shock toxin) genes, agr types, staphylococcal cassette chromosome mec (SCCmec) types and pulsed field gel electrophoresis (PFGE) profiles of a total of 100 non-duplicate methicillin-resistant Staphylococcus aureus (MRSA) bloodstream isolates collected between 2002-2005 at Ankara University Ibn-i Sina Hospital. Antimicrobial susceptibilities were investigated by a semi-automated system (miniAPI, BioMerieux, France); PVL, mecA and toxin (sea, seb, sec, sed, see, seg, seh, sei, sej, tst) genes by polymerase chain reaction (PCR) and SCCmec and agr typing were performed by multiplex PCR. While all isolates were susceptible to vancomycine, aminoglycoside and tetracycline resistance was determined in 91%, ciprofloxacine in 93%, rifampin in 92%, erythromycine in 79% and trimethoprim-sulphametoxazole in 8% of the isolates. mecA gene was detected in all of the isolates, however, PVL positive isolate was not detected. sea was the most frequently (77%) detected enterotoxin gene. SCCmec typing revealed type III in 84 (84%) and agr typing revealed type I in 91 (91%) of the isolates. Multilocus Sequence Typing (MLST) of five representative isolates (two isolates with pattern A, one isolate each from patterns B, C and D) revealed sequence type (ST) 239. This study documented that the dominant MRSA clone in our hospital had SCCmec type III, agr type 1, PVL negative, sea positive and of ST 239. Larger scale intercity and nation wide studies are needed to find out the clonal characteristics of hospital acquired MRSA in Turkey.