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Electronic health records provide the opportunity to assess system-wide quality measures. Veterans Affairs Pharmacy Benefits Management Center for Medication Safety uses medication use evaluation (MUE) through manual review of the electronic health records.To compare an electronic MUE approach versus human/manual review for extraction of antibiotic use (choice and duration) and severity metrics.Retrospective.Hospitalizations for uncomplicated pneumonia occurring during 2013 at 30 Veterans Affairs facilities.We compared summary statistics, individual hospitalization-level agreement, facility-level consistency, and patterns of variation between electronic and manual MUE for initial severity, antibiotic choice, daily clinical stability, and antibiotic duration.Among 2004 hospitalizations, electronic and manual abstraction methods showed high individual hospitalization-level agreement for initial severity measures (agreement=86%–98%, κ=0.5–0.82), antibiotic choice (agreement=89%–100%, κ=0.70–0.94), and facility-level consistency for empiric antibiotic choice (anti-MRSA r=0.97, P<0.001; antipseudomonal r=0.95, P<0.001) and therapy duration (r=0.77, P<0.001) but lower facility-level consistency for days to clinical stability (r=0.52, P=0.006) or excessive duration of therapy (r=0.55, P=0.005). Both methods identified widespread facility-level variation in antibiotic choice, but we found additional variation in manual estimation of excessive antibiotic duration and initial illness severity.Electronic and manual MUE agreed well for illness severity, antibiotic choice, and duration of therapy in pneumonia at both the individual and facility levels. Manual MUE showed additional reviewer-level variation in estimation of initial illness severity and excessive antibiotic use. Electronic MUE allows for reliable, scalable tracking of national patterns of antimicrobial use, enabling the examination of system-wide interventions to improve quality.