The incidence of methicillin-resistant Staphylococcus aureus (MRSA) infective endocarditis (IE) is increasing. This study compared clinical characteristics and mortality in patients with methicillin-sensitive S. aureus (MSSA) IE versus MRSA IE, based on a prospectively collected series of 72 consecutive patients with definite S. aureus IE according to the modified Duke criteria between June 2000 and December 2006. Sixteen of 72 IE patients (22%) were caused by MRSA. Nosocomial origin, surgical site infection, surgery in the previous 6 months, the presence of a catheter and persistent bacteremia were significantly associated with MRSA. MSSA patients had significantly more unknown origin of bacteremia and experienced a significantly higher rate of major embolism than MRSA patients. MSSA patients underwent more frequently combined surgical and antimicrobial therapy, and MRSA patients were treated more frequently with antimicrobial therapy due to a contraindication to surgery. The 6-month mortality was higher in patients with MRSA than MSSA. In the MSSA group treated with antimicrobial therapy without an indication to surgery, all patients survived, and in the combined surgical and antimicrobial group 29% died. The mortality in MRSA patients was lowest if combined surgical and antimicrobial therapy was performed. Both in MSSA and MRSA patients with antimicrobial therapy due to a contraindication to surgery, the mortality was extremely high. These data suggest that in S. aureus IE patients with a nosocomial origin, the presence of a catheter or recent surgery, initial therapy should include antimicrobial agents active against MRSA. Antimicrobial therapy alone with close monitoring of the therapeutic effect and signs of complicated course is an acceptable approach in selected patients with MSSA IE. Denial of surgery because of local or general factors in patients that meet criteria for surgical intervention in acute IE is prognostically ominous.