Eben grew up in Český Krumlov in south Bohemia. He learned to play the piano, and later the cello and organ. Because his father was a Jew he had to leave school in 1943 and spent the rest of the war years in concentration camp in Buchenwald. In the camp he saw many terrible things, including graves into which the Nazis were throwing lots of murdered Jews. These terrible things influenced his music in later years. He had a strong faith and this helped him to survive during 40 years of living in Czechoslovakia under communist rule.