Background Medication errors frequently occur during transitions of care and may have damaging consequences, especially amongst the elderly. Some studies show that quality improvement initiatives with a focus on medication reconciliation have resulted in better health outcomes and a reduced number of readmissions. Objective The primary objective of this study was to quantify and classify medication reconciliation errors detected by a pharmacist and taking place during transitions of care between nursing homes and the health system. Secondary objectives were to assess the relation between error frequency and polypharmacy or between error frequency and the transition type and to describe the medication concerned by this error. Setting Five elderly nursing homes of the health care area in Ferrol (Spain) between January 2013 and December 2017 Method A prospective descriptive study on medication discrepancies found during pharmacist’s medication reconciliation. This was performed at first admission and after every transition of care upon the patient’s return to the nursing home. Interventions were categorized according to the consensus terminology. Main outcome measure Number and type of medication errors, percentage of transitions of care and percentage of patients who suffered at least one reconciliation error were measured. Results At least one medication error was found in 16% of the 2123 studied care transitions, summing up 417 reconciliation errors in 273/981 patients (28%). Wrong dosing (48%) and medication omissions (31%) were the most frequently detected errors. High-risk medication was involved in 40% of the cases. A positive association between polypharmacy (≥ 5 chronic medications) and the frequency of reconciliation errors was found. On the other hand, different transition types did not show a difference in error frequency. Conclusion Reconciliation errors were found in almost 30% of our patients. Unlike other studies, visits to outpatient specialist clinics were included as another type of healthcare transition, encompassing an important percentage of reconciliation errors. The pharmacist helped to reduce these errors in a particularly fragile population such as institutionalized patients.