Verifying which ABAP programs are in use

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An option might be to rename ABAP programs which you expect to no longer be used and create empty ABAP programs instead which pop-up a message such as 'contact … for more information'. This might not be a good option as you might get many complaints.

Another source of information might be the Performance Database (transaction ST03 and STAD).

A good alternative is security and audit logging. Security and audit logging keeps track of all programs and transactions in use. It offers a search engine to look for specific reports, transactions and users. The security portal in the SAP service marketplace (http://service.sap.com/security) contains much more information on how to setup security logging.