2007		Eurydice: She, So Beloved as Director
2007		Alice in Not So Wonderland as Director
2007		Phantom Museums: The Short Films of the Quay Brothers as Director

2005

The Piano Tuner of Earthquakes as Director

2004

Quay Brothers: The Short Films 1979-2003 as Director

2003		The Phantom Museum: Random Forays Into the Vaults of Sir Henry Wellcome's Medical Collection as Director
2003		Songs for Dead Children as Director

2001		Sonic Cinema: Sparklehorse as Director
2001		Stille Nacht V: Dog Door as Director

2000		The Sandman as Director
2000		In Absentia as Director
2000		The Brothers Quay Collection: Ten Astonishing Short Films 1984-1993 as Director

1995		Institute Benjamenta, or This Dream People Call Human Life as Director
1995		The Summit as Director

1993		Stille Nacht IV: Can't Go Wrong Without You as Director
1993		Stille Nacht III: Tales from Vienna Woods as Director
1993		Anamorphosis as Director

1992

Stille Nacht II: Are We Still Married? as Director

1991		The Comb as Director
1991		The Calligrapher as Director

1989

Ex Voto as Director

1988		Rain Dance as Director
1988		Stille Nacht I: Dramolet as Director

1987		Tales of the Brothers Quay as Director
1987		Rehearsals for Extinct Anatomies as Director

1986

Street of Crocodiles as Director

1985

This Unnameable Little Broom as Director

1984		The Cabinet of Jan Švankmajer as Director
1984		The Cabinet of Jan Švankmajer: Prague's Alchemist of Film as Director

1983

Janáček: Intimate Excursions as Director

1982

Igor Stravinsky: The Paris Years Chez Pleyel 1920-1929 as Director

1981		A Fratricide as Director
1981		Punch and Judy: Tragical Comedy or Comical Tragedy as Director
1981		The Eternal Day of Michel de Ghelderode as Director

1979

Nocturna Artificialia as Director

Editing

2025

Sanatorium Under the Sign of the Hourglass as Editor

2011

Through the Weeping Glass: On the Consolations of Life Everlasting (Limbos & Afterbreezes in the Mütter Museum) as Editor

2009

Inventorium of Traces as Editor

2007

Eurydice: She, So Beloved as Editor

1993

Anamorphosis as Editor

1991

The Comb as Editor

1986

Street of Crocodiles as Editor

Sound

2025

Sanatorium Under the Sign of the Hourglass as Sound

2011

Through the Weeping Glass: On the Consolations of Life Everlasting (Limbos & Afterbreezes in the Mütter Museum) as Sound

2009

Inventorium of Traces as Sound Designer

Visual Effects

2025

Sanatorium Under the Sign of the Hourglass as Animation

2022

Ghosts and Whispers as Animation

2013

Unmistaken Hands: Ex Voto F.H. as Animation

2011

Through the Weeping Glass: On the Consolations of Life Everlasting (Limbos & Afterbreezes in the Mütter Museum) as Animation

1993

Anamorphosis as Animation

1991		The Comb as Animation
1991		The Calligrapher as Animation

1986

Street of Crocodiles as Animation

1981		A Fratricide as Animation
1981		Punch and Judy: Tragical Comedy or Comical Tragedy as Animation

Writing

2025

Sanatorium Under the Sign of the Hourglass as Screenplay

2013

Unmistaken Hands: Ex Voto F.H. as Writer

2010

Maska as Writer

2007

Alice in Not So Wonderland as Writer

2005

The Piano Tuner of Earthquakes as Writer

2001

Stille Nacht V: Dog Door as Writer

1995

Institute Benjamenta, or This Dream People Call Human Life as Writer

1991

The Comb as Writer

1986

Street of Crocodiles as Writer

1985

This Unnameable Little Broom as Writer

1981

The Eternal Day of Michel de Ghelderode as Writer