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Gillen has written for both print and online comics. He has worked for Warhammer Monthly and Chaos League.
Since 2003, Gillen has collaborated with artist Jamie McKelvie on a comic strip for the official PlayStation Magazine UK, entitled Save Point.
His 2006 project, described by Gillen as "my first real comic" is another collaboration with McKelvie, the pop-music urban fantasy Phonogram. Veteran comics writer Warren Ellis has dubbed it "one of the few truly essential comics of 2006." The first issue, published by Image Comics, went on sale in August 2006, the first series ran for six issues. The second series ran for seven issues, and was launched in December 2008. A third six-issue series, The Immaterial Girl, exploring the character of Emily Aster, is planned for 2013.
On April 14, 2008 it was announced that Gillen would be collaborating with the artist Greg Scott to expand the Warren Ellis's newuniversal mythos with "a story about killing the future" set in 1959 and he wrote Crown of Destruction, a Warhammer Fantasy comic. The Phonogram sequel "The Singles Club" started in December 2008, a series of one-shots, all about the same night. He also got more work at Marvel with a Dazzler story and a Beta Ray Bill one-shot and mini-series.
His workload at Marvel increased in late 2009. At HeroesCon it was announced he would be writing a Dark Reign tie-in with the Dark Avengers: Ares mini-series. During the 2009 Chicago Comic Con it was announced that Gillen will collaborate with Steven Sanders on a new ongoing series known as S.W.O.R.D from Marvel Comics. Gillen also had a run on Thor, following J. Michael Straczynski, from issues #604 to 614. In late 2010 he started his own ongoing series, Generation Hope, an X-Men spin-off that leads on from the end of the "Second Coming" storyline. Gillen continued on this title until issue #12, being followed by James Asmus.
After collaborating as co-writer with Matt Fraction on Uncanny X-Men beginning with issue #531, Gillen will become sole writer of that title starting with issue #534.1 in 2011. His era of the title saw the Fear Itself event, and a renumbering to #1 in the wake of Schism, and his run will end in a crossover with Avengers vs. X-Men with issue #20. Gillen will write a five-issue miniseries AvX: Consequences, dealing with the aftermath of that event.
In 2011 Gillen returned to Marvel's Asgard, with a run on Journey into Mystery (the original name of Thor, continuing with its original numbering), starting with issue #622. This run finished with #645 in October 2012.
As part of the Marvel NOW re-launch, Gillen will be writing two books - Invincible Iron Man (again taking over from Fraction), with art provided by Greg Land, his penciller on Uncanny, and Young Avengers, with McKelvie.
He has also written a series for Avatar Press called The Heat, and a series for Image called Three, about the helots of Sparta, planned for 2013.