In 2002, she had a supporting role as Reggie Fluty, the officer who first responded to the call for aid for a dying Matthew Shepard, in the Emmy-nominated television film The Laramie Project. In 2005, Madigan starred as Lori Lansky in Winter Passing, directed by Adam Rapp. The following year, she had a supporting role as Patricia Carver, a CIA headquarters analyst, in the Emmy-winning television film The Path to 9/11. In 2007, Madigan played the sister-in-law of Helene (Amy Ryan), Beatrice "Bea" McCready, in the Oscar-nominated film Gone Baby Gone, directed by Ben Affleck. In 2008, she played Dr. Katharine Wyatt on several episodes of ABC's medical drama series Grey's Anatomy. She then guest starred on TNT's crime drama series Saving Grace as Gretchen Lagardi. In 2011, she guest starred in the final episode of TNT's drama series Memphis Beat. In 2016, Madigan starred in the revival of Sam Shepard's play Buried Child for The New Group at the Pershing Square Signature Center. The show transferred to the West End's Trafalgar Studios in November 2016, where Madigan reprised her role as Halie.