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Aim To identify whether patients with congestive cardiac failure have a higher prevalence of inaccurately documented medications on general practice referral letters to emergency departments than other polypharmacy patients. Method A prospective case-control study was undertaken in two urban emergency departments. Patients with a general practitioner referral letter and a history of congestive cardiac failure were recruited as the study group, while patients with a general practitioner referral letter and a history of polypharmacy were recruited as controls. Medications on the referral letter were compared with those dispensed by the patient's usual pharmacist (gold standard) and emergency clinician documentation. Discrepancies were analysed by number, type and potential severity. Results A total of 205 patients were recruited: 69 patients with heart failure in the study group and 136 patients in the control group. The proportion of letters with at least one discrepancy was high in both groups (91 vs 88%, p = 0.57). On average, heart failure patients had more discrepancies per letter (4.8 vs 3.8, p = 0.05). The most common discrepancy in all groups was over-inclusion of medications (68% heart failure and 64% control). Heart failure patients had more discrepancies judged likely to be harmful (24 vs 14%, p < 0.001). Discussion The prevalence of medication discrepancies in referral letters to the emergency department is very high. The overall prevalence of a discrepancy was not higher in heart failure patients compared with other polypharmacy patients, but there were more discrepancies per letter and these discrepancies were potentially more serious. Extra vigilance is required when reconciling medications for patients with heart failure because of higher numbers and greater potential severity of medication discrepancies.