CD "Heino Eller - works for violin and piano", First Hand Records (2024). Andres Kaljuste (violin), Sophia Rahman (piano)
CD "Heino Eller. Complete Piano Music. Volume Nine", Toccata Classics (2023). Sten Lassmann (piano)
CD "Heino Eller. Complete Piano Music. Volume Eight", Toccata Classics (2022); Sten Lassmann (piano)
CD "Heino Eller. Complete Piano Music. Volume Seven", Toccata Classics (2021); Sten Lassmann (piano)
CD "Heino Eller. Symphonic Poems", Ondine (2019); Estonian National Symphony Orchestra, conductor Olari Elts
CD "Heino Eller. Violin Concerto. Fantasy. Symphonic Legend. Symphony No. 2", Ondine (2018); Baiba Skride (violin), Estonian National Symphony Orchestra, conductor Olari Elts
CD "Heino Eller. Complete Piano Music. Volume Six", Toccata Classics (2018); Sten Lassmann (piano)
CD "Heino Eller. String Quartets", ERR (2016). Tallinn String Quartet
CD "Heino Eller. Complete Piano Music. Volume Four", Toccata Classics (2013); Sten Lassmann (piano)
CD "Heino Eller. Complete Piano Music. Volume Three", Toccata Classics (2013); Sten Lassmann (piano)
CD "Heino Eller. Complete Piano Music. Volume Two", Toccata Classics (2012); Sten Lassmann (piano)
CD “Heino Eller. Complete Piano Music. Volume One”, Toccata Classics (2011); Sten Lassmann (piano)
CD "3 prelüüdi" [3 Preludes], Eesti Muusikaakadeemia (2005); Heljo Sepp (piano)
CD "Kodumaine viis" [Native Air], Heljo Sepp (2004); Heljo Sepp (piano)
CD "Neenia", ECM Records (2001); Tallinn Chamber Orchestra, Tõnu Kaljuste (conductor)
CD "Dreizehn Klavierstücke über estnische Motive; Glocken; Sonate für Klavier solo Nr. 1", Antes Edition (2001); Aleksandra Juozapénaité-Eesmaa (piano)
CD "Violin concerto; symphonic poems", Bella Musica (1999); Viktor Pikaizen (violin), Eesti Ringhäälingu Orkester (Estonian Broadcast Orchestra), Peeter Lilje, Vello Pähn (conductor).
CD "The Heino Eller school", Finlandia Records (1998); Ostrobothnian Chamber Orchestra, Juha Kangas (conductor)
CD "Complete preludes", Pro Piano Records (1998); Vardo Rumessen (piano)
CD "Sümfoonilist loomingut" [Symphonic Pieces], Forte (1994); Estonian National Symphony Orchestra, Peeter Lilje (conductor)