Background Medication errors represent the most common type of error that compromises patient safety, with approximately 20% believed to result in harm. Over 40% of these errors are believed to result from inadequate medication reconciliation during admission, transfer, and discharge of patients and many of these errors could be prevented if adequate medication reconciliation processes were in place. In an effort to minimize adverse events caused during these care transitions, the Joint Commission has stated medication reconciliation as one of its National Patient Safety Goals and health care providers and organizations are encouraged to perform the process at various patient care transitions. Objective Identify the types of medication discrepancy that occurred during medication reconciliation performed by a pharmacist gathering the best possible medication history (BPMH). Estimate the potential for harm with each medication discrepancy using the severity rating methods developed by Cornish et al. (Arch Intern Med 165(4):424-429, 2005). Setting Tertiary care hospital in Jeddah, Saudi Arabia. Method Prospective 3-month study on 286 adult patients, admitted for at least 24 h and regularly taking at least four chronic prescription medications. Medication histories taken by physicians and by a pharmacist gathering the BPMH were compared. Identified discrepancies were reviewed by a panel of clinical pharmacists to assess the potential to cause patient harm with these errors. Main Outcome measure Number and types of medication discrepancies recorded by the pharmacist. Results Total number of medications recorded by physicians was 2548, versus 3085 by the pharmacist. 48.3% of patients had at least one unintended medication discrepancy by physicians. 537 medication discrepancies were reported (17.4% of number of medication discrepancies recorded by pharmacist). Types of medication discrepancies included, omissions (77% of discrepancies), commissions (13%), dosing errors (7%), and frequency errors (3%). 52% of the identified medication discrepancies had the potential to cause moderate to severe patient discomfort. Conclusion Patient medication histories are frequently recorded inaccurately by physicians during admission of patients which results in medication-related errors and compromises patient safety. Medication reconciliation is crucial in reducing these errors. Pharmacists can help in reducing these medication-related errors and the associated risks and complications.