Abstract: An integrated pharmacy system receives prescription information, creates a substitution reference list identifying the requested medical item and a plurality of equivalent medical items, automatically selects one of the items identified on the substitution reference list, fills the prescription, checks the accuracy of the filled prescription, facilitates the sales exchange, and creates an archive of the transaction, although not all steps need to be performed for every application. The integrated pharmacy system can also prevent unauthorized users from performing improper functions such as, for example, attempting to dispense an item which is not a proper substitute for the requested item. The present invention, by automatically substituting equivalent medical items for a requested medical item and by automatically archiving each prescription transaction, simplifies the prescription filling and record keeping requirements for the pharmacy technician and pharmacist.