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