Having delved into Cite_body.php, I've come accross this (Cite_body.php:569) # The following assumes that the parsed <ref>s sent within # the <references> block were the most recent calls to # <ref>. This assumption is true for all known use cases, # but not strictly enforced by the parser. It is possible # that some unusual combination of #tag, <references> and # conditional parser functions could be created that would # lead to malformed references here. If I comment out line 582: $this->rollbackRef( $type, $ref_key, $ref_group, $ref_index ); Then my references reappear, albeit with no counts (and therefore the links from article to references and visa versa don't work) So, it would appear that the parser is parsing the <ref> calls within the <references> block before it parses the <ref>'s in the templates above. Leaving that line uncommented, I've tried reformatting templates in various ways to attempt to stumble accross something which the parser can parse in the order indended, but I haven't found any combination of template changes which helps. I'll continue to dig in Cite and try and come up with a bugfix, but as unfamiliar with the internals of Cite as I am, if anyone has any tips they would be greatly appreciated. Thanks Andru On 2013-03-19 09:50:27 +0000, Andru Vallance said: