It wasn't long afterwards that Gleeson landed his first screen role, either, playing a quarryman in Jim Sheridan's "The Field" (1990). Over the course the next five years, he played his share of small roles, like a policeman in "Far and Away" (1992) and a bar patron in "The Snapper" (1993). Although he had won notice for his rendition of Irish patriot Michael Collins in the TV production "The Treaty" (shown in the USA in 1998), Gleeson lost the role to the better-known Liam Neeson in Neil Jordan's 1996 biopic and instead was cast in a supporting part. Jordan made it up to the actor by casting him in the pivotal role of a caring priest in "The Butcher Boy" (1998). But it was Gleeson's back-to-back portrayals of two very different thieves that solidified his standing as a performer of note. In "I Went Down" (1998), he offered a rich comic turn as the sideburn-wearing, cowboy-obsessed and dim-witted Bunny, a low-level gangster forced to work with a recently released prisoner (Peter McDonald). On the heels of that deft performance came the tour de force as true-life Irish criminal Martin Cahill in John Boorman's "The General" (also 1998). Gleeson bore an uncanny physical resemblance to Cahill which only added additional layers to his well-wrought characterization with Cahill emerging as a complex figure, at once charming and moral yet also capable of extreme brutality.

Gleeson displayed his impressive range as the titular "Sweety Barrett" (1998), an illiterate circus performer who runs afoul of a corrupt policeman. Further adding to his rising profile, Gleeson was cast as a Rupert Murdoch-like mogul in John Woo's sequel to the Tom Cruise vehicle "Mission: Impossible" (2000). The actor reunited with John Boorman for the spy drama "The Tailor of Panama" (2001) and was tapped by director Steven Spielberg for the role of Lord Johnson-Johnson in the sci-fi parable "AI: Artificial Intelligence" (2001) before teaming with Irish director Danny Boyle for the offbeat, post-modern zombie film "28 Days Later" (2002) and made an appearance as Monk, a survival-minded Irish immigrant, in director Martin Scorsese's bloody epic "Gangs of New York" (2002). Gleeson delivered a particularly menacing turn as a thoroughly corrupt police official in "Dark Blue" (2003). That same year, he was seen in the sci-fi thriller "28 Days Later" and turned in a winning performance as Stobrod, the once-abusive, now-penitent father of earthy Ruby (Renee Zellweger) in "Cold Mountain" (2003) before moving on to action-epic territory with his role as Menelaus in "Troy" (2004) and the popcorn thriller genre as a grieving father in M. Night Shyamalan's "The Village" (2004).

Gleeson next appeared in Wolfgang Petersen’s “Troy” (2004), playing Menelaus, king of Sparta, whose wife, Helen (Diane Kruger), is kidnapped by Paris, the prince of Troy (Orlando Bloom). Despite the presence of Brad Pitt as über-warrior Achilles and a massive budget with which to launch a thousand ships, the movie failed to please a majority of critics, though box office totals—particularly overseas—made critical calls of mediocre filmmaking and lackluster performances moot. He then played a prominent member of the South African police who ran torture chambers during apartheid in the John Boorman drama, “In My Country” (2005), starring Samuel L. Jackson and Juliette Binoche. Gleeson then appeared in “Kingdom of Heaven” (2005), Sir Ridley Scott’s evenhanded take on the Crusades of the 12th century. Following a supporting role in “Breakfast on Pluto” (2005), Neil Jordan’s strange tale about the exploits of Patrick Braden (Cillian Murphy), a tough, but deceptive transvestite bounding about 1970’s London, Gleeson made his first appearance as Alastor “Mad Eye” Moody in “Harry Potter and the Goblet of Fire” (2005).