Discrepancies between electronic prescribing systems and patients' actual use of medicines can result in adverse events and medication errors and have serious consequences for the patients. The discrepancies can be identified when performing a thorough medication reconciliation. Computerized health care systems throughout the Danish health care sector are integrated with the Shared Medication Record (SMR). In the SMR, current medication and medication prescriptions are registered. The aim of this study was to evaluate the number and types of discrepancies between medications listed in the SMR and an updated medication list, obtained through a thorough medication reconciliation, for patients admitted in Danish hospitals. Pharmacists listed the number and type of discrepancies for 412 patients. A total of 1,004 discrepancies were registered, with a mean number of 2.4 medication discrepancies per patient. For 25% (n = 101) of the patients, no discrepancies were found, 20% (n = 86) had one discrepancy, and 16% (n = 66) had five or more discrepancies. More than 50% of the patients had one or more medications in the SMR that the patient did not administer, and 12.6% used medications that were not listed in the SMR. This shows that the SMR should not be used as the only source of information when recording medication history.