The <journal-id> element holds an external identifier, typically assigned to a journal by a publisher, archive, or library to provide a unique identifier for the journal. The contents of this element should not be confused with the @id attribute, which holds an internal document identifier that can be used by software to perform a simple link inside the document.

There may be more than one such identifier, with the type of identifier named by the @journal-id-type attribute. For example, one identifier may be a registered DOI, another a control number assigned by the publisher, and another the journal abbreviation assigned by PubMed Central.

For NLM’s PubMed Central and other NLM-internal processing, this element contains an alternative to, or short form of, the journal title, used to identify the journal domain. In such processing, this element is the equivalent to, and usually used instead of, the <abbrev-journal-title> element. Outside PubMed Central processing, this use of the <journal-id> element is rare; journal tag sets typically use the <abbrev-journal-title> element to hold the short version of a journal title and the <issn> element to hold a journal identifier, rather than creating a separate identifier for the journal. For journals that have assigned an non-ISSN identifier (typically numeric) for individual journal titles, this <journal-id> element can hold that identifier.