Background A recently introduced computerised physician order entry system (CPOES) in hospital and a primary care electronic record system help prescribing and provide information about patients' medicines. These tools should improve the reconciliation process and diminish potential errors associated with chronic medication. Purpose The aim of this study is to describe and analyse the discrepancies between chronic medication recorded on the electronic health record system and the prescription of this medication upon admission to hospital. Materials and methods From March through May 2011, information was collected about patients admitted older than 60 years with chronically-prescribed medication and an updated preadmission treatment file. The pharmacist compared the computerised prescriptions with the current chronic medication listed by the prescription program (e-Osabide). Chronic medication data were verified with the patient primary care electronic record system (GlobalClinic). If discrepancies were found the admission reports were checked to decide if they were justified. Unjustified discrepancies were reported and classified as reconciliation errors. Results Chronic treatment of 88 patients was analysed (average age: 73.3 years. 48 women, 40 men). 33 patients were admitted as emergencies (E), 26 to surgical wards (S) and 29 to medical wards (NS). The average number of chronically-prescribed medicines per patient prescribed at admission were 7.3 and 5.4, respectively. 32 unjustified discrepancies were found (26.1% of patients, 0.36 per patient). Classified by route of admission: E, 24.2% of patients (0.42/patient); S, 30.8% (0.38); NS, 24.1% (0.28). By reconciliation errors: dose/frequency incorrect (21), omission (6), added medicine (5). The acceptance of interventions made was 56.3% (18/32). Conclusions The integration of CPOES and the electronic healthcare record system makes the reconciliation process easier and reduces prescription errors. With recently introduced CPOES incomplete prescriptions are no longer a problem. However, preventable prescription errors associated with reconciliation occur due to not using the tools now available.