OBJECTIVES: Evaluate the incremental impact of S. aureus infection stays on hospital charges and length-of-stay in U.S. hospitals in 2003. METHODS: The 2003 Nationwide Inpatient Sample data were analyzed. Hospital discharges were classified as either a S. aureus–related infection stay or a non-S. aureus-related infection stay using a combination of several ICD-9 codes. Incremental effect of S. aureus infection on hospital charges and length-of-stay was estimated using multivariate regression models adjusting for hospital fixed effects and patient variables including age, gender, race, payer, diagnosis-related grouping and concomitant conditions including diabetes, dialysis and lung disease. RESULTS: S. aureus infection was reported as a discharge diagnosis for 1.0% of all hospital inpatients, or 389,963 stays, in 2003. S. aureus infection hospital stays were significantly more likely among male, older patients, stays that were paid by Medicare, white or non-Hispanics and hospital stays among individuals with diabetes, lung disease or dialysis. After adjusting for covariates, the mean incremental impact of S. aureus infection on hospital charges and length-of-stay was $37,251 (95% Confidence Interval (CI): $34,678 - $39,823) and 8.2 days (95% CI: 7.9 - 8.5) among all inpatient stays, $40,637 (95% CI: $37,683 - $43,591) and 9.2 days (95% CI: 8.8 – 9.6) among surgical stays, $83,952 (95% CI: $75,853 - $92,052) and 16.8 days (95% CI:15.7 – 17.9) among invasive cardiovascular stays, $34,202 (95% CI: $29,612 - $38,791) and 9.6 days (95% CI: 9.0 – 10.2) among invasive orthopedic stays and $119,292 (95% CI: $106,209 - $132,374) and 19.8 days (95% CI: 17.5 – 22.2) among invasive neurosurgical stays. CONCLUSION: S. aureus infections present a considerable economic burden to U.S hospitals. Based on the prevalence of S. aureus infection and its incremental impact, the total economic impact of S. aureus among all hospital admissions was estimated at $14.5 billion in 2004 U.S. dollars.