In 1987, while an MFA student at Bard College, Haynes made a short, Superstar: The Karen Carpenter Story, which chronicles the life of American pop singer Karen Carpenter, using Barbie dolls as actors. The film presents Carpenter’s struggle with anorexia and bulimia, featuring several close-ups of Ipecac (the nonprescription drug Carpenter was reputed to have used to make herself vomit during her illness). Carpenter’s chronic weight loss was portrayed by using a “Karen” Barbie doll with the face and body whittled away with a knife, leaving the doll looking skeletonized. The film is also notable for staged dream sequences in which Karen, in a state of deteriorating mental health, imagines being spanked by her father.

Haynes’ 1991 feature film debut, Poison, garnered Haynes further acclaim and controversy. Drawing on the writings of gay writer Jean Genet, the film is a triptych of queer-themed narratives, each adopting a different cinematic genre: vox-pop documentary (“Hero”), 50s sci-fi horror (“Horror”) and gay prisoner romantic drama (“Homo”). The film explores traditional perceptions of homosexuality as an unnatural and deviant force, and presents Genet’s vision of sado-masochistic gay relations as a subversion of heterosexual norms, culminating with a marriage ceremony between two gay male convicts. Poison marked Haynes’ first collaboration with his longtime producer Christine Vachon.

Haynes’ next project was Mildred Pierce, a five-hour miniseries for HBO based on the novel by James M. Cain and the 1945 film starring Joan Crawford. The series starred Kate Winslet in the title role and featured Guy Pearce, Evan Rachel Wood, Melissa Leo, James LeGros and Hope Davis. Filming was completed in mid-2010 and the series began airing on HBO on 27 March 2011. It received 21 Primetime Emmy Award nominations, winning five, and Winslet won a Golden Globe Award for her performance.

Haynes is set to direct an untitled Peggy Lee film based on a screenplay by Nora Ephron, starring Reese Witherspoon. He is also developing a TV series based on the 2012 documentary The Source Family for HBO.

An edited book of personal interviews was published in 2014, titled Todd Haynes: Interviews.

On October 20, 2017, Haynes’s Wonderstruck was released, having premiered at the 2017 Cannes Film Festival on May 18, 2017. The film is an adaptation of Brian Selznick’s children’s book of the same name. Wonderstruck stars Julianne Moore and is produced by Haynes’ collaborator Christine Vachon and Amazon Studios, which is also distributing the film. The movie describes two deaf children, one in 1927 and the other in 1977, who embark on separate quests to find themselves. When asked why he’d made a children’s movie, in his October 15, 2017, NPR interview, Haynes explained, “I felt like it spoke to something indomitable about the nature of kids and the ability for kids to be confronted with challenges and the unknown and to keep muscling through those challenges.”

Haynes directed a film titled Dark Waters for Participant Media. The film is based on Nathaniel Rich’s The New York Times Magazine article “The Lawyer Who Became DuPont’s Worst Nightmare,” which is about corporate defense attorney Robert Bilott and his environmental lawsuit against the American conglomerate DuPont. Mark Ruffalo and Anne Hathaway will star in the film. Principal photography began in January 2019, in Cincinnati. It was released on November 22, 2019.