Even if Panton-Valentine leukocidin (PVL), toxic shock syndrome toxin-1 (TSST-1), staphylococcal enterotoxins (SEB and SEC), and exfoliative toxins (ETA and ETB) may be associated with severe infections, the clinical significance of their presence in clinical isolates of Staphylococcus aureus remains poorly documented. In this study, we evaluated the prevalence of toxin genes and the relationship between their presence and the severity of infection. We screened for the presence of these six toxin genes among 186 consecutive S. aureus clinical isolates (resistant or not to methicillin) during a two-month period. We compared the toxin gene profile between strains recovered from patients presenting uncomplicated infections (n = 151) and from patients suffering from severe infections (n = 35). At least one toxin gene was detected in 55 (29.6%) isolates as follows: pvl (n = 1), tst + sec (n = 5), seb (n = 19), seb + sec (n = 1), sec (n = 28), and eta (n = 1). The proportion of toxin-producing strains among patients with uncomplicated infections (27.8%) and patients with severe infections (37.1%) was not statistically different (p = 0.3044), even if the severity of infection tended to be associated with the presence of sec (p = 0.0655). Although the prevalence of toxin genes was relatively high herein, no statistically significant association between the severity of infection and the presence of toxin genes was observed.