Il Duetto (film) 1970
Der Loop der Loop (film) 1970
Palais en Flammes (film) 1970
Nocturna Artificialia: Those Who Desire without End (film) 1979
Punch and Judy: Tragical Comedy or Comical Tragedy (film) 1980
Ein Brudermord/A Fratricide [adaptors; based on the short story by Franz Kafka] (film) 1981
The Eternal Day of Michel de Ghelderode 1898–1962 (film) 1981
Igor—The Paris Years Chez Pleyel (film) 1983
†Leoš Janáček: Intimate Excursions (film) 1983
†The Cabinet of Jan Švankmajer—Prague's Alchemist of Film (film) 1984
†Little Songs of the Chief Officer of Hunar Louse, or This Unnameable Little Broom (Being a Largely Disguised Reduction of the Epic of Gilgamesh) Tableau II [adaptors; based on the poem cycle The Epic of Gilgamesh (film) 1985; also known as This Unnameable Little Broom and The Epic of Gilgamesh
†Street of Crocodiles [adaptors; based on various writings by Bruno Schulz] (film) 1987
Rehearsals for Extinct Anatomies (film) 1988
Stille Nacht (film) 1988
The Pond (film) 1989
De Artificiali Perspectiva or Anamorphosis (film) 1991; also known as Anamorphosis
The Comb: From the Museums of Sleep, Fairytale Dramolet to Scenes and Texts by Robert Walser (film) 1991; also known as The Comb
Ex Voto (film) 1991
‡Stille Nacht II (film) 1992
§Long Way Down (Look What the Cat Drug In) (film) 1993
¦Stille Nacht IIIA: Tales from the Vienna Woods (film) 1993
Stille Nacht IV (film) 1993
Institute Benjamenta, or This Dream Which People Call Human Life [adaptors; based on the novel Jakob von Gunten by Robert Walser] (film) 1996
∗In addition to the works listed above, the Brothers Quay have designed sets and stages for opera productions; these include The Love for Three Oranges (1988), A Flea in Her Ear (1989), Mazeppa (1991), and Le bourgeois gentilhomme (1992).
†These works are included in the compilation film The Brothers Quay (1987).
‡This short film was produced for the musical group His Name Is Alive to accompany the song "Are We Still Married?"
§This short film was produced for musician Michael Penn to accompany his song "Look What the Cat Drug In."
¦This short film was produced for the musical group His Name Is Alive to accompany the song "Can't Go Wrong without You."