We investigated the virulence gene carriage and molecular type characteristics of Staphylococcus aureus isolates from bloodstream infections (BSIs) and skin and soft tissue infections (SSTIs) in children. A total of 71 isolates, 16 of which were methicillin-resistant S. aureus (MRSA), were investigated by PCR for virulence-associated gene profiles, sequence type and spa type. This revealed that 76·7% and 53·7% of the SSTI and BSI isolates, respectively, exhibited simultaneous carriage of ⩾10 virulence genes. Compared to BSI isolates, carriage rates for hla, hlb, cna, clfA, seb, sec and pvl genes were significantly higher in SSTI isolates. By contrast, carriage of eta, etb and sea was significantly higher for BSI isolates. Thirty-four sequence types (STs) and 36 spa types were identified in the 71 isolates and included 14 novel STs and four novel spa types. ST59-MRSA-IV/V-t437 was the most common clone in the MRSA isolates. We concluded that virulence determinants are widely distributed in isolates of S. aureus strains from children with BSIs and SSTIs, with an unexpectedly high rate in SSTI isolates. Future profiling of S. aureus virulence determinants may allow the prediction of severity and outcome for children with these infections.