While numerous studies have assessed the outcomes of methicillin-resistant S. aureus (MRSA) colonization over the short term, little is known about longer-term outcomes after discharge. An assessment of long-term outcomes could provide information about the utility of various MRSA prevention approaches. A matched-cohort study was performed among Veterans Affairs (VA) patients screened for MRSA colonization between the years 2007 and 2009 and followed to evaluate outcomes until 2010. Cox proportional-hazard models were used to evaluate the association between MRSA colonization and long-term outcomes, such as infection-related readmission and crude mortality. A total of 404 veterans were included, 206 of whom were MRSA carriers and 198 of whom were noncarriers. There were no culture-proven MRSA infections on readmission among the noncarriers, but 13% of MRSA carriers were readmitted with culture-proven MRSA infections on readmission (P < 0.01). MRSA carriers were significantly more likely to be readmitted, to be readmitted more than once due to proven or probable MRSA infections, and to be readmitted within 90 days of discharge than noncarriers (P < 0.05). Infection-related readmission (adjusted hazard ratio [HR] ‫؍‬ 4.07; 95% confidence interval [CI], 2.16 to 7.67) and mortality (adjusted HR ‫؍‬ 2.71; 95% CI, 1.87 to 3.91) were significantly higher among MRSA carriers than among noncarriers after statistically adjusting for potential confounders. Among a cohort of VA patients, MRSA carriers are at high risk of infection-related readmission, MRSA infection, and mortality compared to noncarriers. Noncarriers are at very low risk of subsequent MRSA infection. Future studies should address whether interventions such as nasal or skin decolonization could result in improved outcomes for MRSA carriers.