Gilligan became the third BBC casualty on Friday when he followed chairman Gavyn Davies and director-general Greg Dyke out of the BBC.
It is believed that Gilligan will return to a job in newspapers and is already reported to be in discussions with Associated Newspapers about a job on the Mail on Sunday.
In a 500-word statement issued to the press, Gilligan said that his departure was his own initiative and he reiterated the claim in his story that the government did sex up its weapons of mass destruction dossier.
"My departure is at my own initiative. But the BBC collectively has been the victim of a grave injustice. If Lord Hutton had fairly considered the evidence he heard, he would have concluded that most of my story was right.
"The government did sex up the dossier, transforming possibilities and probabilities into certainties, removing vital caveats; the 45-minute claim was the 'classic example' of this; and many in the intelligence services, including the leading expert in WMD, were unhappy about it," his statement read.
Gilligan already has connections with the Mail on Sunday. Last year the paper published his follow-up piece to the 'Today' broadcast, which accused the government of lying and knowing that the 45-minute claim was untrue.
Another possible option for Gilligan is a return to The Sunday Telegraph. He spent five years at The Sunday Telegraph working on the foreign news desk and as the newspaper's defence correspondent prior to joining the BBC in 1999, when he was hired by former 'Today' editor Rod Liddle to bring some edge to the programme.
However, he quickly made enemies of members of the government and earned a reputation for being arrogant and a maverick.
There is also speculation that now Gilligan has left the BBC he will capitalise on his notoriety and write a book about his role in the Dr Kelly affair.
Gilligan started his career on the Cambridge Evening News where he worked from 1994 to 1995.
While at 'Today', Gilligan posed undercover to buy anti-personnel landmines in contravention of the 1998 Landmines Act; exposed the relative ease with which it was possible to get postal votes on behalf of dead people; and obtained a series of damning leaked official reports about Britain's performance in the Kosovo war.
He also broke the story of the RAF's £1bn combat jet that could not drop precision bombs and was the first British journalist to report on the EU's controversial plans for a Charter of Fundamental Rights.
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