Purpose To investigate the extent of medication discrepancies (MDs) revealed by medication reconciliation (MR) and to assess the potential clinical relevance of the MDs for the patients in a short-term and long-term perspectives.

Methods Patients ≥18 years admitted to five internal medicine wards were included in this prospective study. MDs between the medication list obtained by physicians at hospital admission and medication list obtained by a structured MR process by pharmacists were identified and assessed for clinical relevance by an expert team. Clinical relevance was assessed in two ways as (a) if they were not acted upon during the hospital stay (short term) or (b) if they persisted after discharge from the hospital (long term).

Results In total 262 patients, age 19–98 (SD 18.94, mean 73.4 years), 58.8% female, were included. 79.4% of the patients had at least one MD with a mean of 3.2 MDs/patient. 80.7% of the MDs were discussed with the physician, and 95.5% of these were acted upon. Of the 438 MDs evaluated by the expert panel, 35.2% and 71.2% were assessed to be of moderate, major or extreme clinical relevance in the short-term and long-term perspectives, respectively.

Conclusions By using a structured approach, MDs were identified for 80% of the patients and the majority of the MDs were evaluated to possibly harm the patient in a long-term perspective. The results emphasise that structured MRs may improve patient safety.

Trial registration number 2011/542.