In recent years, Chinlund has been seen in several independent projects, notably A Brother's Kiss (1997). He also served as the executive Producer of the film, which was directed by childhood friend Seth Zvi Rosenfeld. A Brother's Kiss was filmed in and around the neighborhood where Chinlund and Rosenfeld grew up. The film tells the story of two brothers, Lex (Chinlund) and Mick (Michael Raynor), who grow up in the hard streets of New York. Chinlund continued in his long vein of independent features with roles in Chutney Popcorn (1999), Amy's Orgasm (2001), Goodnight Joseph Parker (2004) and Sinner (2007).

Chinlund guest starred on The X-Files second-season episode "Irresistible" playing serial killer Donnie Pfaster, for which he garnered major critical acclaim. In 2000 he had a small role in episode two of Gilmore Girls. In 2002 he had a recurring role in two episodes of Buffy The Vampire Slayer: "Listening to Fear" and "Into the Woods".

Chinlund has starred in big-screen movies including Tears of the Sun (2003), Con Air (1997), The Chronicles of Riddick (2004), directed by David Twohy, who also directed Chinlund in the underwater thriller Below (2002), and Ultraviolet (2006). He also reprised his X-Files role as Donnie Pfaster for a seventh-season episode entitled "Orison". Chinlund was also in Training Day, Eraser and The Legend of Zorro.

As with his film roles, he played villainous roles in those two shows, most notably as a defense attorney and an unethical Journalist in the original Law & Order, and a serial killer in Special Victims Unit. Chinlund also played an American-Indian Casino President and CEO, "Chief Doug Smith" in the fourth-season episode "Christopher" of the hit HBO original series, The Sopranos. In 2009, he made an appearance on Castle in the first-season episode "Home Is Where The Heart Stops". In 2010, he made an appearance on House in the sixth-season episode titled "The Down Low", playing a drug dealer named Eddie.