| 1992 | Symphony no. 4 / Symphony no. 5 | Vagn Holmboe; Jutland Opera Choir, Aarhus Symphony Orchestra, Owain Arwel Hughes | | 1 |
| 1992 | Symphony no. 6 / Symphony no. 7 | Vagn Holmboe; Aarhus Symphony Orchestra, Owain Arwel Hughes | | 1 |
| 1993 | Works for A Cappella Choir | Vagn Holmboe; Sokkelund Sangkor, Morten Schuldt-Jensen | | 1 |
| 1993 | String Quartets, Vol. 1 | Vagn Holmboe; The Kontra Quartet | | 1 |
| 1994 | Symphony no. 1 / Symphony no. 3 / Symphony no. 10 | Vagn Holmboe; Aarhus Symphony Orchestra, Owain Arwel Hughes | | 1 |
| 1995 | Symphony no. 8 / Symphony no. 9 | Vagn Holmboe; Aarhus Symphony Orchestra, Owain Arwel Hughes | | 1 |
| 1995 | Symphony no. 2 / Sinfonia "In Memoriam" | Vagn Holmboe; Aarhus Symphony Orchestra, Owain Arwel Hughes | | 2 |
| 1995 | Works for Organ | Borup-Jørgensen, Maegaard, Hvidtfelt Nielsen, Gudmundsen-Holmgreen, Holmboe; Eva Feldbæk | | 1 |
| 1996 | String Quartets, Vol. II: Nos. 2, 5 and 6 | Vagn Holmboe; The Kontra Quartet | | 1 |
| 1996 | Symphony no. 11 / Symphony no. 12 / Symphony no. 13 | Vagn Holmboe; Aarhus Symphony Orchestra, Owain Arwel Hughes | | 1 |
| 1996 | Complete Chamber Concertos, Vol. I: Nos. 1-3 | Vagn Holmboe; Anne Øland, Niels Thomsen, Mikkel Futtrup, Eva Østergaard, The Danish Radio Concert Orchestra, Hannu Koivula | | 1 |
| 1996 | The Complete Symphonies | Vagn Holmboe; Aarhus Symphony Orchestra, Owain Arwel Hughes | | 1 |
| 1996 | Brass Concertos | Vagn Holmboe; Håkan Hardenberger, Christian Lindberg, Jens Bjørn-Larsen, Aalborg Symphony Orchestra, Owain Arwel Hughes | | 2 |
| 1997 | Complete Chamber Concertos, Vol. II: Nos. 4-6 | Vagn Holmboe; Anne Øland, Mikkel Futtrup, Tim Frederiksen, Niels Ullner, The Danish Radio Concert Orchestra, Hannu Koivula | | 1 |
| 1997 | String Quartets, Vol. III: Nos. 7, 8 and 9 | Vagn Holmboe; The Kontra Quartet | | 1 |
| 1997 | Complete Chamber Concertos, Vol. III: Nos. 7-9 | Vagn Holmboe; Max Artved, Mikkel Futtrup, Tim Frederiksen, The Danish Radio Sinfonietta, Hannu Koivula | | 1 |
| 1998 | Concertos for Recorder and Flute | Vagn Holmboe; Dan Laurin, Manuela Wiesler, Aalborg Symphony Orchestra, Owain Arwel Hughes | | 1 |
| 1998 | String Quartets, Vol. IV: Nos. 10, 11 and 12 | Vagn Holmboe; The Kontra Quartet | | 1 |
| 1998 | Complete Chamber Concertos, Vol. IV: Nos. 10-13 | Vagn Holmboe; Jacques Mauger, Ole Edvard Antonsen, Max Artved, Tim Frederiksen, The Danish Radio Sinfonietta, Hannu Koivula | | 1 |
| 1999 | String Quartets, Vol. V: Nos. 13, 14 and 15 | Vagn Holmboe; The Kontra Quartet | | 1 |
| 2000 | String Quartets, Vol. VI: Nos. 17, 19 and 20 | Vagn Holmboe; The Kontra Quartet | | 1 |
| 2000 | String Quartets, Vol. VII: Nos. 16 and 18 / Sværm and Quartetto Sereno | Vagn Holmboe; The Kontra Quartet | | 1 |
| 2002 | Requiem for Nietzsche | Vagn Holmboe; Helge Rønning, Johan Reuter, The Danish National Radio Symphony Orchestra and Choir, Michael Schønwandt | | 1 |
| 2004 | Sinfonias I-IV | Vagn Holmboe; Danish Radio Sinfonietta, Hannu Koivula, Søren Elbæk, Troels Svane | | 1 |
| 2007 | Mikkelborg: Everything Matters / Jersild: 10 Impromtu / Holmboe: Duo Concertato / Koppel: Duo for Violin and Guitar | Palle Mikkelborg, Jørgen Jersild, Vagn Holmboe, Herman David Koppel; Kim Sjøgren | | 1 |
| 2009 | Works for Violin and Piano | Vagn Holmboe; Johannes Søe Hansen, Christina Bjørkøe | | 1 |
| 2009 | Danish Violin Concertos, Vol 5 | Eyvind Andersen, Niels Viggo Bentzon, J. L. Emborg, Leif Thybo, Vagn Holmboe; Kai Laursen | | 1 |
| 2012 | Chamber Symphonies | Vagn Holmboe; Lapland Chamber Orchestra, John Storgårds | | 1 |
| 2013 | Concertos | Vagn Holmboe; Norrköping Symphony Orchestra, Dima Slobodeniouk, Erik Heide, Lars Anders Tomter | | 1 |
| 2014 | Nordic Concertos | Anders Hillborg, Vagn Holmboe, Karin Rehnqvist, Bernhard Crusell; Martin Fröst | | 1 |
| 2021 | String Quartets Vol. 1 | Vagn Holmboe; Nightingale String Quartet | | 1 |
| 2022 | String Quartets, Vol. 2 | Vagn Holmboe; Nightingale String Quartet | | 1 |
| 2024 | String Quartets, Vol. 3 | Vagn Holmboe; Nightingale String Quartet | | 1 |
