Background. Staphylococcus aureus is a common cause of disease, particularly in colonized persons. Although methicillin-resistant S. aureus (MRSA) infection has become increasingly reported, population-based S. aureus and MRSA colonization estimates are lacking. Methods. Nasal samples for S. aureus culture and sociodemographic data were obtained from 9622 persons ⩾1 year old as part of the National Health and Nutrition Examination Survey, 2001–2002. After screening for oxacillin susceptibility, MRSA and selected methicillin-susceptible S. aureus isolates were tested for antimicrobial susceptibility, pulsed-field gel electrophoresis clonal type, toxin genes (e.g., for Panton-Valentine leukocidin PVL), and staphylococcal cassette chromosome mec (SCCmec) type I–IV genes. Results. For 2001–2002, national S. aureus and MRSA colonization prevalence estimates were 32.4% (95% confidence interval CI, 30.7%–34.1%) and 0.8% (95% CI, 0.4%–1.4%), respectively, and population estimates were 89.4 million persons (95% CI, 84.8–94.1 million persons) and 2.3 million persons (95% CI, 1.2–3.8 million persons), respectively. S. aureus colonization prevalence was highest in participants 6–11 years old. MRSA colonization was associated with age ⩾60 years and being female but not with recent health-care exposure. In unweighted analyses, the SCCmec type IV gene was more frequent in isolates from participants of younger age and of non- Hispanic black race/ethnicity; the PVL gene was present in 9 (2.4%) of 372 of isolates tested. Conclusions. Many persons in the United States are colonized with S. aureus; prevalence rates differ demographically. MRSA colonization prevalence, although low nationally in 2001–2002, may vary with demographic and organism characteristics.