Klein was born into a Moravian Jewish family in Přerov and, showing musical talent early, studied piano with Růžena Kurzová and Vilém Kurz, and composition with Alois Hába (in 1939–1940). He was forced to discontinue his studies in 1940 at the university when the Nazis closed all institutions of higher learning following their occupation of Czechoslovakia in March 1939. Since compositions and performances by Jewish musicians were banned, his own works could not be played, though he managed to perform as a concert pianist under several aliases for a time, a.o. under the name of Karel Vranek. In 1940 he was offered a scholarship at the Royal Academy of Music in London, but by that time anti-Jewish legislation prevented his emigration.
In December 1941 he was deported by the Nazis to Terezín concentration camp, where along with Leoš Janáček's pupil Pavel Haas, Hans Krása, and Schoenberg's pupil Viktor Ullmann he became one of the major composers in that camp, one of the few in which artistic activity occurred on any scale. His works from these years include music for string quartet (similar in tone to Berg's opus 3 work), a string trio, and a piano sonata among others. Klein performed also as solo pianist at least on 15 recitals, and he participated also in chamber music performances (member of piano trio, piano quartet).
He was deported to Auschwitz and then to Fürstengrube in October 1944, less than two weeks after completing his string trio. He died under unclear circumstances during liquidation of the Fürstengrube camp in January 1945.
His work was influenced by Alois Hába, Alban Berg, and particularly by Leoš Janáček. He used melody from Janáček's Zápisník zmizelého as a theme in his Divertimento (1940).
Recordings on Northeastern and on Koch International Classics, for example, have allowed modern listeners to evaluate the quality of his compositions of the 1940s.
- Four Movements for String Quartet (1936–1938), CHF
- Duo for Violin and Viola in the Quarter-Tone System (1940)
- Divertimento for Eight Wind Instruments (1940)
- Three Songs for High Voice and Piano, Opus 1 (1940)
- String Quartet, Opus 2 (1941)
- Duo for Violin and Cello (1941) unfinished
- Madrigal for Two Sopranos, Alto, Tenor and Bass to words by François Villon, Czech translation by Otokar Fischer (1942) 2'
- The First Sin, for male voice choir on a Czech folk poem (1942) 4'
- Fantasy and Fugue for String Quartet (1942–1943) 8'
- Piano Sonata (1943), PA 9'
- Madrigal for Two Sopranos, Alto, Tenor and Bass to words by Franz Holderlin, Czech translation by Erich A Saudek (1943) 3'
- Trio for Violin, Viola and Cello (1944) 11'
- Partita (Trio for Violin, Viola and Cello in arrangement for chamber orchestra by Vojtěch Saudek)
- Slavický, Milan: Gideon Klein. A Fragment of Life and Work. Praha: Helvetica Tempora 1995. ISBN 80-902124-5-X (Czech version of the book ISBN 80-902124-0-9)
- Kuna, Milan: Hudba vzdoru a naděje. Terezín 1941–1945. Praha: Editio Bärenreiter 2000. H 7822
- Vysloužil, Jiří: Hudební slovník pro každého II. Vizovice: Lípa, 1998 ISBN 80-86093-23-9
- Nadace Gideona Kleina - Gideon Klein Foundation
- Music and the Holocaust - Gideon Klein
- Gideon Klein - Czech Composer
- Page on Gideon Klein
- Comprehensive discography of Terezin Composers by Claude Torres
- Czech Jewish Museum
- Concert 7 Candles to commemorate Terezín composers Gideon Klein and Pavel Haas
- Further reading and listening on Terezín: The Music 1941-44