Niki> I tried playing around with \bibliographystyle, but this seems
Niki> to have no affect on font size. 
  
Jean-Marc>  I am surprised. AFAIK, ams styles are the only ones which use a
Jean-Marc>  font for references which is smaller than the document font. 
Jean-Marc>  Are you sure that bibtex has been re-run which you changed
Jean-Marc>  bibliography style?


I'm not sure if I'm using Bibtex corectly with LyX but
here's what happens:

I have a Latex \bibliography command at the end of my document.
When doing View->dvi there's an entry in the TOC for Bibliography
but the bibliography does not get generated at the end of the
document.  

If I then add a Latex \bibliographysytle{plain} command right before
the \bibliography command, the biblography gets generated but
in the small font which you said is due to AMS.

I finally succeeded in generating a Bibliography with a larger font
by doing Export->LaTex and then running LaTex manually on exactly 
the same document.  So the style of the Bibliography appeared 
differently depending on whether the dvi file was generated manually
or within LyX.  
-- 

        Nick



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