Introduction Medication discrepancies are associated with adverse drug events. Electronic health records (EHRs) may reduce discrepancies, especially if integrated with pharmacy dispensing. We determined the prevalence of discrepancies within a national healthcare system with EHR–pharmacy linkage to characterise the medications involved and to identify factors associated with discrepancies.

Methods We conducted a retrospective cohort study of ambulatory care patients at Veterans Affairs Boston Healthcare System, April 2010–July 2011. The primary outcome was the presence of any medication discrepancy or specific types of discrepancies: commission—present in the record but not taken by patient; omission—not present in the record; duplication—present more than once; or alteration in dose or frequency—present but taken differently than documented.

Results Sixty-two patients (60%) had at least one medication discrepancy. Prevalence of commissions, omissions, duplications and alterations were 36%, 27%, 11% and 19%, respectively. The involved medications differed by type of discrepancy, but non-opioid analgesics and herbal therapies were common among commissions and omissions. In adjusted analyses, an increasing number of medications was associated with more commissions (OR 1.2; 95% CI 1.1 to 1.3) and duplications (OR 1.2; 95% CI 1.1 to 1.4) and fewer omissions (OR 0.9; 95% CI 0.8 to 1.0).

Discussion In a system with a well established EHR linked to pharmacy dispensing, medication discrepancies occurred in 60% of ambulatory clinic patients. Patients with a greater number of medications were more likely to have errors of commission and duplication, but less likely to have errors of omission. Our findings highlight that relying on EHRs alone will not ensure an accurate medication list and stress the need to review medication taking thoroughly with patients to capitalise on the full potential of EHRs.