To investigate the prevalence, the antibiotic resistance pattern and the population structure of Staphylococcus aureus, S. aureus isolates from the anterior nostrils of patients of general practitioners (GPs) were analysed. Insight into the S. aureus population structure is essential, as nasal carriers of S. aureus are at increased risk of developing an S. aureus infection. S. aureus was isolated from nasal swabs from 2691 patients with no sign of an infection collected in 29 GP practices in The Netherlands. The susceptibility pattern for several classes of antibiotics was determined, as well as the S. aureus genetic background, using spa typing. S. aureus was isolated from 617 of the 2691 (23%) nasal swabs. The prevalences of resistance to ciprofloxacin, co-trimoxazole, fusidic acid, macrolides and mupirocin were 0.2%, 0%, 6%, 5% and 1%, respectively. Half of the isolates were associated with a genetic background common to the major methicillin-resistant S. aureus (MRSA) clones, e.g. clonal complex (CC)1, CC5, CC8, CC22, CC30 and CC45, and the remainder were mainly associated with CC7, CC12, CC15, CC26, CC51 and CC101. The low prevalences of resistance suggest that, in the Dutch situation, S. aureus isolates from patients visiting their GP because of complaints not related to infection do not represent a large reservoir of antibiotic resistance genes. Although no MRSA isolates were found, the genetic background of some of the S. aureus isolates is commonly observed among community-associated (CA)-MRSA clones (CC1, CC8 and CC30), and this might suggest that these isolates have the potential to become CA-MRSA.