Koteas' acting teacher Peter Masterson believed in his pupil, directing him in "Full Moon in Blue Water", in which he was convincing as an emotionally disturbed handyman, and the bomb "Blood Red" (both 1988). For Roos and Francis Ford Coppola, he appeared in "Gardens of Stone" (1987) and "Tucker: A Man and His Dream" (1988), in the latter as an earnest young car designer. His dark Mediterranean good looks helped secure the role of young Ari in the ABC miniseries "The Richest Man in the World: The Aristotle Onassis Story" (1988), and Koteas has performed in two of fellow Canadian Atom Egoyan's films, "The Adjuster" (1992), as the amoral title character, and "Exotica" (1994), as a disc jockey in a strip club romancing one of the dancers.

Koteas portrayed Casey Jones, man among terrapins, in the 1990 surprise blockbuster "Teenage Mutant Ninja Turtles" and returned for the aptly named third installment "Teenage Mutant Ninja Turtles III" (1993) prior to the release of David Cronenberg's controversial "Crash" (1996). Koteas' unique and off-beat persona readily lent itself to the pivotal role of Vaughn, whose unhealthy fascination with post-crash wounds had him presiding over a loosely knit group of auto accident fetishists recreating notorious crack-ups. He also acted in two Danny De Vito-produced vehicles, the sci-fi "Gattaca" (1997, Andrew Niccol's directing debut), seen briefly in the opening sequences as the father of Ethan Hawke's character, and "Living Out Loud" (1998), an adaptation from the Chekhov canon, in which he appeared in a particularly vivid scene as a stranger who kisses Holly Hunter.

Terrence Malick offered Koteas one of his finest screen opportunities to date as the conscience-afflicted captain of "The Thin Red Line" (also 1998), adapted by Malick from the Guadalcanal novel by James Jones. Playing a thoughtful lawyer and decent officer of Charlie Company whose desire to protect his men puts him at odds with the superior (Nick Nolte) who sees soldiers simply as cannon fodder on the road to personal glory, Koteas provided one of the few well-rounded characters in the director's much-anticipated return to filmmaking. He also turned up earlier that year as a demonic serial killer in "Fallen" and shared the screen with Ian McKellen as a mysterious bum in Bryan Singer's "Apt Pupil", based on the Stephen King novella. Koteas followed by supporting Winona Ryder and Ben Chaplin in cinematographer Janusz Kaminski's thriller "Lost Souls" (2000).

In 2002, Koteas was cast in the dram-edy feature "Simone," which co-starred Al Pacino and Catherine Keener, and then went on to portray the character Ali in the drama feature "Ararat."