The aim of this article is to describe the methods used to develop the medication reconciliation programme implemented in a tertiary care hospital, and to discuss the main problems encountered and lessons learned during the process. A quasi-experimental study was carried out, analysing discrepancies between routine medication and drugs prescribed in the hospital, before and after an electronic reconciliation tool was introduced at admission. This tool was integrated into the computerized provider order entry system. The implementation of the electronic reconciliation tool has shown a reduction of the rate of discrepancies, decreasing from 7.24% (CI 95% 6.0–8.5) before the intervention to 4.18% (CI 95% 3.2–5.1) afterwards. Projects like this are costly, but this study has made it possible to detect numerous areas where interventions could be useful and proved the importance of a medication reconciliation programme.