The SE39 transaction is used to compare two ABAP’s in split screen mode. This can be two ABAP programs in single system, or by clicking on the button Compare Different Systems between two systems. With the cross system comparison the tool will ask for which RFC to use.
Usage of SE39
Start transaction SE39. In this example we will take a copy of a standard SAP BAPI and compare it with the original (to find clones, read this blog):
Press display to compare. Initially not much happens, except source code on the left and right.
Press the Comparison On button:
Result now shows the delta’s with indicators on the left side of the screen:
Use the buttons Next difference from cursor and the other button to quick jump through the code to find the differences.
References
Bug fix notes:
3539141 – Splitscreeneditor: Error for empty source in version management
3564002 – SE39: improve handling of inactive programs
3568037 – Enhancements are not being displayed in SE39 for remote systems



