An automated tracking system for a pharmacy that maintains each medication's Unique Drug Identifier (“UDI”) from the stock supply container to individual prescription orders filled therefrom and provides a security system for determining a discrepancy associated with filling a prescription order. The UDI information automatically travels with each individual prescription until it is dispensed to a customer or patient, thereby allowing the system to monitor and track supply containers and individual prescription orders for improper or potentially fraudulent transactions. If desired, the improved security allows both supply containers and individual prescription orders to be stored in the same storage area thereby maximizing available storage space while still improving dispensing and filling accuracy and minimizing loss.