Difference Engine repertoire is drawn from performances and work in rehearsal. It represents the ensemble in base instrumentation as violin and piano and also as expanded instrumentation for two players, such as in Stockhausen's Tierkreis which was performed by two players on six instruments: violin, electric violin, viola, keyboards, piano and vibraphone.
Also included are ensemble performances of HPSCHD by John Cage for three harpsichords and computer generated tapes, The Sinking of the Titanic by Gavin Bryars and Knee Play 5 from the opera Einstein on the Beach, by Philip Glass.
- Wolfgang Amadeus Mozart - Sonata in A Major KV 305
- Anton Webern - Vier Stucke
- Michael Nyman - Music from ‘Drowning by Numbers
- Henryk Mikolaj Gorecki - Mala Fantaja
- Frank Bridge - Moto Perpetuo
- Francis Poulenc - Movements Perpetuels
- James MacMillan - After the Tryst
- Henry Purcell - Sonata in G Minor
- Elisabeth Jacquet de la Guerre - Violin Sonata
- Charles Ives - Sonata No. 4 for Violin and Piano
- Bohuslav Martinu - Sonatina
- Bohuslav Martinu - Intermezzo
- Carolan - Farewell to Music
- Joe Hughes - Itch
- Gavin Bryars - Incipit Vita Nova
- Gavin Bryars - The North Shore
- Gavin Bryars - The Sinking of the Titanic
- Bela Bartok - Gyermekenek
- Arvo Part - Spiegel im Spiegel
- Jean Sibelius - Die Glocken
- Cesar Frank - Melancholie
- Erik Satie - Choral hypocrite
- Maurice Ravel - Berceuse
- Igor Stravinsky - Chanson Russe
- Arcangelo Corelli - Sonata in D Major
- Ralph Vaugh-Williams - Six English Folk Songs
- Franz Schubert - Sonatina No. 1
- Keith Jarrett - Elegy
- Philip Glass - Knee Play 5
- Alan Hovhaness - Campuan Sonata for Viola and Piano
- Michael Jon Fink - Vocalise
- Karlheinz Stockhausen - Tierkreis