Stallman, who is also head of the GNU Project, was accused of making sexist remarks during a keynote he gave at a joint conference of the KDE and GNOME projects held in Gran Canaria, Spain, earlier this year.
The remarks, for which he copped an enormous amount of flak , were: "And we also have the cult of the virgin of emacs. The virgin of emacs is any female who has not yet learned how to use emacs. And in the church of emacs we believe that taking her emacs virginity away is a blessed act."
After the summit, Stallman was criticised by many people, with GNOME advisory board member David Schlesinger, Canonical chief technology officer Matt Zimmerman and Red Hat developer Matthew Garrett being prominent among those who attacked him.
In a post to the GNOME Foundation mailing list on Saturday, Stallman wrote: "Some of the people in the audience in my speech in the Gran Canaria Desktop Summit thought that my joke about the Virgin of Emacs was intended to make some kind of statement about women.
He said he was surprised by this reaction, "since I had told the same joke dozens of times and this is the first report of interpreting it that way."
Stallman said this was a misunderstanding as "the only intended meaning of the Cult of the Virgin of Emacs is to parody another Cult of the Virgin. The whole St IGNUius (sic) routine makes fun of me, the free software movement and religion, through parody."
The St IGNUcius routine is one that Stallman goes through at many of his talks, dressed in a black robe and wearing a computer disk on his head. At times the routine falls flat as he is not the best teller of a joke.
Stallman said that his views about women vis-a-vis free software were that they deserved freedom in using computers, the same as men did.
"Some women already appreciate this freedom and have become free software activists. We need more people, regardless of sex, to do this, so that someday all women, and all men, will enjoy the freedom that free software offers.
Stallman added that "to help avoid misunderstandings of this kind in the future, since August I have changed the joke so that the Virgin of Emacs can be of either sex."