Well-characterized Staphylococcus aureus nasal and blood isolates (N = 429) were tested by polymerase chain reaction for the prevalence of genes that encode leukocidal toxins. The leukotoxin genes lukE+lukD were found at high prevalence, significantly more so in blood (82%) than in nasal isolates (60.5%). Although almost all isolates were positive for the gamma-hemolysin gene, none was positive for lukM. Genes encoding Panton-Valentine leukocidin (PVL) components were very rare in either nasal or blood isolates. The lukE+lukD-negative isolates were significantly more likely to be positive for the staphylococcal enterotoxin gene combination seg/sei (89.5%) and the toxic shock syndrome toxin-1 gene (39.3%) than lukE+lukD-positive isolates (41.7% and 12.7%, respectively). The lukE+lukD-negative isolates were also more likely to show positivity for the accessory gene regulatory locus agr III, but less likely to be positive for the agr II locus. The co-possession of different virulence factors and their probable synergy should receive more attention in order to better understand their role in pathogenicity.