Between 1994 and 2002, he created The Cremaster Cycle, a series of five films described by Jonathan Jones in The Guardian as "one of the most imaginative and brilliant achievements in the history of avant-garde cinema.

A full-scale survey of Barney's work through Drawing Restraint 9 was held at the San Francisco Museum of Modern Art in 2006 and included over 150 objects of varying media.

The piece was part of a benefit art show and auction titled "Good Wood", raising awareness and funds for Power House Productions' Ride It Sculpture Park in Detroit, Michigan.

The riding was performed on site by skateboarder Lance Mountain, documented by photographer Joe Brook and published by Juxtapoz Magazine in their February 2013 issue.

[15] Matthew Barney's epic Cremaster cycle (1994–2002) is a self-enclosed aesthetic system consisting of five feature-length films that explore processes of creation.

As the cycle evolved over eight years, Barney looked beyond biology as a way to explore the creation of form, employing narrative models from other realms, such as biography, mythology, and geology.

[18] River of Fundament takes the form of a three-act opera and is loosely based on Norman Mailer’s novel Ancient Evenings.

[19] In collaboration with composer Jonathan Bepler, Barney combines traditional modes of narrative cinema with filmed elements of performance, sculpture, and opera, reconstructing Mailer’s hypersexual story of Egyptian gods and the seven stages of reincarnation, alongside the rise and fall of the American car industry.

[19] The film’s central scene is an abstraction of Mailer’s wake, set in a replica of the late author’s apartment in Brooklyn Heights and featuring Maggie Gyllenhaal, Paul Giamatti, Elaine Stritch, Ellen Burstyn, Peter Donald Badalamenti II, Joan La Barbara, and jazz percussionist Milford Graves.

[21] The Yale University Art Gallery debuted Redoubt on March 1, 2019, alongside an exhibition of large bronze and brass sculptures and electroplated engravings inspired by the film.

The pieces REN and Guardian of the Veil revisit the language of the Cremaster Cycle, via a ritualistic exploration of Egyptian symbolism inspired by Norman Mailer's novel Ancient Evenings.

[24] In June 2009, a collaboration between Barney and Elizabeth Peyton, titled Blood of Two, was performed for the opening of the Deste Foundation's exhibition space, the Slaughterhouse, located on the Greek island Hydra.

[25][26] In June 2017, Barney, local art curator Brandon Stosuy,[27] and other artists[28] installed Remains Board on his studio in Long Island City.

The board is a large seven-segment digital clock,[29] visible from the United Nations and midtown Manhattan, counting down the days, hours, and minutes remaining in the U.S. president Donald Trump's first term.

On inauguration day in 2021, at 12:00 p.m., Haela Hunt-Hendrix of Liturgy performed a guitar solo beneath the Remains Board as the clock began to approach 00:00:00.

[32] For the season 2000/2001 in the Vienna State Opera, Barney designed a large scale picture (176 sqm) as part of the exhibition series "Safety Curtain", conceived by museum in progress.

"River of Fundament" was considered the largest filmic project since the Cremaster Cycle and first major museum solo exhibition in Los Angeles.

"It feels more like a very energetic longing for a beginning, in which all kinds of imagery have been put to the service of one man's intricate fantasy of return to the womb.

When he brings his boundless imagination to a subject he goes down to its depths to create images and implant ideas that stay in your mind for ever" writes art historian Richard Dorment in The Daily Telegraph.