During this time he formed the Tartu school of composition, which gave rise to many composers, including Eduard Tubin.

The list of his pupils offers the best proof of this: each of them has created a distinguished original style.

Among his students were Els Aarne, Anatoli Garšnek [et], Alfred Karindi, Villem Kapp, Boris Kõrver, Karl Leichter, Leo Normet, Uno Naissoo, Eduard Oja, Valter Ojakäär, Arne Oit, Arvo Pärt, Boris Parsadanian, Alo Põldmäe, Kaljo Raid, Jaan Rääts, Olav Roots, Lepo Sumera and Eduard Tubin.

[2] Heino Eller was married to pianist Anna Kremer, who was executed at a concentration camp by German occupational authorities in 1942 because of her Jewish ethnicity.

His musical language contains many national traits, but he was influenced by 20th-century styles as diverse as impressionism and expressionism.