Children with sickle cell anaemia (SCA) might carry hospital-associated bacterial lineages due to frequent hospital stays and antibiotic treatments. In this study we compared Staphylococcus aureus from SCA patients (n = 73) and healthy children (n = 143) in a cross-sectional study in Gabon. S. aureus carriage did not differ between children with SCA (n = 34, 46·6%) and controls matched for age, residence and sex (n = 67, 46·9%). Both groups shared similar S. aureus genotypes. This finding points towards a transmission of S. aureus between both groups in the community. We conclude that resistance rates from population-based studies with healthy participants could therefore also be used to guide treatment and prophylaxis of endogenous infections in children with SCA despite a different selection pressure.