OBJECTIVE To determine the impact of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus (MRSA/VRE) designations, or flags, on selected hospital operational outcomes. DESIGN Retrospective cohort study of inpatients admitted to the Massachusetts General Hospital during 2010-2011. METHODS Operational outcomes were time to bed arrival, acuity-unrelated within-hospital transfers, and length of stay. Covariates considered included demographic and clinical characteristics: age, gender, severity of illness on admission, admit day of week, residence prior to admission, hospitalization within the prior 30 days, clinical service, and discharge destination. RESULTS Overall, 81,288 admissions were included. After adjusting for covariates, patients with a MRSA/VRE flag at the time of admission experienced a mean delay in time to bed arrival of 1.03 hours (9.63 hours [95% CI, 9.39-9.88] vs 8.60 hours [95% CI, 8.47-8.73]). These patients had 1.19 times the odds of experiencing an acuity-unrelated within-hospital transfer [95% CI, 1.13-1.26] and a mean length of stay 1.76 days longer (7.03 days [95% CI, 6.82-7.24] vs 5.27 days [95% CI, 5.15-5.38]) than patients with no MRSA/VRE flag. CONCLUSIONS MRSA/VRE designation was associated with delays in time to bed arrival, increased likelihood of acuity-unrelated within-hospital transfers and extended length of stay. Efforts to identify patients who have cleared MRSA/VRE colonization are critically important to mitigate inefficient use of resources and to improve inpatient flow. Infect Control Hosp Epidemiol 2016;37:782-790.