PubMed now includes DOIs in its records - see NLM Technical Bulletin article for more details. In the tagged MEDLINE format, the DOI is in a field called LID, according to this bulletin. I have done a quick PubMed search and found the DOI appearing as AID, however.
A quick test suggests that AID goes to the DOI field in RefWorks, and the Electronic Resource Number field in EndNote 9.
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