Background: Medication errors are common and can compromise patient safety. Commonly seen at discharge, they can be identified and resolved even during admission. Medication reconciliation is recommended to prevent errors arising from medication discrepancies. Aim: To conduct medication reconciliation in two multispeciality hospitals and classify the identified medication discrepancies according to their potential to cause harm. Materials and Methods: This prospective interventional study was carried out in medicine and surgery departments of two urban hospitals over a period of six months. Patients who satisfied the criteria were enrolled and medication reconciliation was performed. Interventions were provided whenever necessary. The identified discrepancies were then given to an expert panel for classifying them based on their potential to cause harm. Results: 580 medication discrepancies were identified from a total 372 patients, drug interaction (n=345, 61.6%) was the most commonly observed discrepancy, followed by omission error (n=127, 12.9%). The medication discrepancies observed from both the hospitals were found to be statistically not significant (p=0.246). From a total of 580 discrepancies, 454 (78.27%) discrepancies were Significant, 80 (13.79%) Serious and 46 (7.93%) Not Significant. Conclusion: The results of our study show that there are discrepancies in medication use when the patient transitions in a hospital. It is recommended that medication reconciliation practices be performed by clinical pharmacist during the hospital stay to ensure continuity of healthcare and for patient safety. An electronic medical record capable of capturing and continuously updating medication information may be a long-term solution. To achieve this, professional development of clinical pharmacists is of paramount importance.