Medication errors are common, fatal, costly but preventable. Location of drugs on the shelves and wrong drug names in prescriptions can cause errors during dispensing process. Therefore, a good drug-shelf arrangement system in pharmacies is crucial for preventing medication errors, increasing patient’s safety, evaluating pharmacy performance, and improving patient outcomes. The main purpose of this study to suggest a new drug-shelf arrangement for the pharmacy to prevent wrong drug selection from shelves by the pharmacist. The study proposes an integrated structure with three-stage data mining method using patient prescription records in database. In the first stage, drugs on prescriptions were clustered depending on the Anatomical Therapeutic Chemical (ATC) classification system to determine associations of drug utilizations. In the second stage association rule mining (ARM), well-known data mining technique, was applied to obtain frequent association rules between drugs which tend to be purchased together. In the third stage, the generated rules from ARM were used in multidimensional scaling (MDS) analysis to create a map displaying the relative location of drug groups on pharmacy shelves. The results of study showed that data mining is a valuable and very efficient tool which provides a basis for potential future investigation to enhance patient safety.