2000–10: Six Feet Under and Law & Order
From 2001 to 2005, he portrayed Billy Chenowith in the HBO drama series Six Feet Under. For that work, he was twice nominated for the Screen Actors Guild Award for Outstanding Performance by an Ensemble in a Drama Series along with his co-stars. Sisto starred in the 2001 drama film Angel Eyes, alongside Jennifer Lopez. In 2003, Sisto starred in the drama film Thirteen, the romantic comedy The Movie Hero, and the horror film Wrong Turn. That same year, he also appeared in the series finale of The WB's teen drama series Dawson's Creek. Sisto then performed on the Los Angeles stage, playing the role of bigoted Southerner Shane Mungitt in Richard Greenberg's play Take Me Out, about a baseball player who announces he is gay; Sisto was nominated for a Los Angeles Drama Critics Circle Award for his role.
In 2006, he appeared in the Broadway play Festen at the Music Box Theatre. In the same year, he starred in the short-lived NBC drama series Kidnapped, top-lined the direct-to-video mystery horror film Population 436, and starred in the crime-thriller film Unknown. In July 2007, Sisto was featured in the Maroon 5 video for the song "Wake Up Call". He played a man who was sleeping with the girlfriend of Adam Levine. That same year, he appeared as Earl Hunterson opposite Keri Russell in the comedy-drama film Waitress.
In 2008, Sisto joined the cast of the NBC crime drama series Law & Order, as Detective Cyrus Lupo, replacing Milena Govich's Detective Nina Cassady as the partner of Jesse L. Martin's Ed Green. Sisto had already appeared on the show, as a lawyer, in the previous season's finale. Sisto stayed on for the series' next three seasons, and his character became partners with Anthony Anderson's Detective Kevin Bernard after Martin left the series near the end of season 18. Also in 2008, Sisto starred in the drama film Gardens of the Night, and voiced the role of Batman in the direct-to-video film Justice League: The New Frontier. In 2009, he played a Catholic priest, alongside Kristin Chenoweth as a prostitute, in the independent drama film Into Temptation. The following year, he starred in the Manhattan Theatre Club production of Spirit Control at the New York City Center, gaining rave reviews for his performance as Adam Wyatt.