The skin commensal Staphylococcus epidermidis has become one of the most important causative agents of nosocomial infections associated with medical devices. Differentiation between invasive S. epidermidis and its commensal counterpart is crucial for clinical decision making. The ica gene locus, which codes for production of polysaccharide intercellular adhesion (PIA), represents a frequently suggested molecular marker for infectivity. Our data demonstrated that production of PIA was not significantly increased among clinical strains, which may explain the controversial results obtained previously on the correlation of ica presence with origin from infection. Therefore, in this study, we attempted to identify novel genes discriminating between invasive and commensal strains based on the comparison of genome sequences. Our results indicated that the bacterial insertion sequence element IS256 occurred significantly more frequently in strains of clinical origin. Importantly, IS256 might thus constitute a molecular marker to discriminate invasive strains from commensal strains of S. epidermidis.