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Pathogenic factors of Staphylococcus aureus (SA) in the development of infective endocarditis (IE) have not been sufficiently investigated. The purpose of this study was to analyze the pathogenesis and virulence factors of SA in patients with IE as compared to patients with uncomplicated bacteremia (un-BAC). This is a retrospective case-control study (2002-2014) performed at a tertiary hospital in Spain. Clinical and epidemiological factors were analyzed. We assessed the presence of toxin genes [toxic shock syndrome toxin 1 (tst-1) and enterotoxins A (etA), B (etB), and D (etD)] and the potential relationship between accessory gene regulator (agr) groups and the development of IE confirmed by polymerase chain reaction (PCR). Twenty-nine patients with IE were compared with 58 patients with uncomplicated S. aureus bacteremia (SAB). As many as 75.9 % of patients had community-acquired IE (p < 0.005). Multivariate analysis revealed that there is a significant relationship between community-acquired infection and severe sepsis or septic shock and IE. Also, a minimum inhibitory concentration (MIC) of vancomycin ≥1.5 μg/ml was found to be associated with IE. The agr group I was prevalent (55.2 % vs. 31.0 %; p = 0.030). No association was observed between toxin genes (tst-1, etA, etB, and etD) and IE. The superantigen (SAg) most frequently found in SA isolates was tst-1 (12.6 %). We found no association between toxin genes and IE, probably due to the small sample size. However, a direct relationship was found between agr I and the development of IE, which suggests that agr I strains may have more potential to cause IE.