Go to Tools > Open Term Lists > Journals Term Lists
If there are journals listed on the Terms tab, delete them. Caveat: if you’ve already entered a unique abbreviation (e.g., for a non-MEDLINE journal), don’t delete that term!
On the Lists tab (with Journals highlighted), click Import List…
Browse to the Medical Journals Term List. Look for it in C:\Program Files\EndNote X2\Terms Lists\Medical.txt.
You’ll see the Terms List updating with 1,000’s of MEDLINE journal abbreviations.
It can take a few minutes for the new abbreviations to kick in. If you don’t eventually see the abbreviations, make sure the Output Style is set to use the journal abbreviation.
If the journal name in your reference within the library doesn't match up exactly with the full name or one of the abbreviations in the terms list, the substitution will not take place. Compare the journal name in your reference to the terms in the term manager and make sure you have an exact match. If the journal name is not in the terms list it will show in red. A single space or the inclusion of a period at the end of the name is enough for it to not be considered a match.