If you have EndNote X4 or later...

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Click on References > Find Duplicates.
EndNote will begin going through your library and bring up pairs of references which it thinks are duplicates. It will present you with a handy side-by-side comparison so you can quickly determine which reference you'd rather keep. You can also copy and paste information between the references so that the one you keep has all the data you need.

Alternatively you can press Cancel on the the side-by-side comparison and all suspected duplicates will appear in a Duplicate References group.


How Does EndNote Detect a Duplicate?
Click Edit > Preferences (Windows) or EndNote > Preferences (Mac) and click 'Duplicates' on the left - here you can set which fields you want EndNote to look at, and how strict you want it to be.

Why Doesn't EndNote Automatically Delete References?
Your data is important - you wouldn't want any bibliographic software to discard any reference data without you having checked it first.


Any Tips?
If you only have a few obvious duplicates, you can easily delete them manually by holding Ctrl on your keyboard and clicking on the duplicates you wish to delete to select multiple references, then press delete or drag to the Trash

Keep an eye on your Record Number - earlier (lower) Record Numbers are more likely to have been cited in documents, and you don't want to delete it in case you need to work on that document again.


What Do I Do If I Delete a Reference Which Has Been Cited?
Firstly, don't panic. When you come to re-format the document EndNote will ask you to re-insert the missing reference - you simply choose the reference with the 'new' Record Number.


What About Older Versions of EndNote?
With EndNote X2 and before, the 'Find Duplicates' feature will either highlight all the references it thinks are duplicates, or present the suspected duplicates in a separate group. The side-by-side comparison feature was introduced with EndNote X3, and copy-and-paste between the screens was introduced with X4.