A method and system for processing financial instruments to detect the presence of duplicate instruments. The method may include the steps of receiving items of information for a plurality of financial instruments, grouping the items into cycles and appending cycle and time dependent information to the items to form coded items, storing the coded items in a database, comparing the items to find items having duplicate identifying information, marking duplicate items for subsequent deletion and printing a report listing the duplicate items. The system may include a mainframe, data repository, item processing applications, and a module that filters items from incoming strings to remove false positives. The remaining duplicate items may be viewed on a graphical user interface that allows a user to review attributes of each item and manually mark duplicates for subsequent deletion.