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 1939–40). He was forced to abort his university studies in 1940 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 performed, though he managed to perform as a concert pianist under several aliases for a time, e.g., under the pseudonym 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 at that camp. he initially gave concerts in secret, but the camp became one of the few in which artistic activity was eventually permitted by Nazis on any scale, if only to deceive the broader public as to their real intentions. 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. Moreover, Klein performed as solo pianist at approximately 15 recitals, and also participated in chamber music performances (member of piano trio, piano quartet).
Klein was deported to Auschwitz in October 1944 and then to Fürstengrube, a coal-mining labour camp, in October 1944, less than two weeks after completing his string trio. He died under unclear circumstances during the liquidation of the Fürstengrube camp in January 1945. he had confided his manuscripts to Irma Semtska, his Therienstadt girlfriend, before leaving, and they were turned over to his sister Eliska at waar's end.
His work was influenced by Alois Hába, Alban Berg, and particularly 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)
- Joseph Way (1997). "Fuguemasters.com". Retrieved 25 November 2011.
- David Bloch. "Music and the holocaust". Retrieved 25 November 2011.
- Rodney Winther, An Annotated Guide to Wind Chamber Music, Alfred Music 2004 p.141
- Lucy Miller Murray, Chamber Music:An Extensive Guide for Listeners, Rowman & Littlefield 2015 p.237.
- Kuna, p. 117
- 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