Most of the severe bacterial infections originate from the endogenous microflora of human body surfaces. However, the molecular basis of colonization, e.g. of the human nose by Staphylococcus aureus, has remained incompletely understood. Several surface-exposed proteins and wall teichoic acid (WTA) polymers have previously been implicated in S. aureus attachment to nasal epithelial cells. Here we dissect the role of these molecules in colonization using S. aureus sortase A (srtA) and tagO mutants deficient in surface protein and WTA display, respectively. Although the two mutants were similarly affected in attachment to nasal cells they were abrogated in binding to different types of epithelial ligands. Surface protein sorting, but not WTA, were required for keratin- or fibronectin-mediated interactions while only WTA-mediated binding to nasal cells was effectively inhibited by polyinosinic acid, indicating a possible role of scavenger receptor-like molecules in WTA-dependent epithelial interactions. Both mutants exhibited profound colonization defects in a cotton rat nasal colonization model, albeit at different stages of colonization (>90% reduced bacterial counts at 24h or several days after inoculation with the tagO or srtA mutant, respectively). These data indicate that S. aureus nasal colonization is a multifactorial process with various ligands affecting initial colonization and prolonged persistence in different ways. Our studies should be useful in the development of new preventive and therapeutic strategies.