A footnote is defined in a paragraph that is started by a footnote marker in square brackets in column 0, no indentation allowed. The footnote reference is simply the marker in square brackets, inside text. For example:
The Org homepage[fn:1] now looks a lot better than it used to.
...
[fn:1] The link is: http://orgmode.org
The following commands handle footnotes:
Further reading
Chapter 2 of the manual
Sacha Chua's tutorial