| 1994 | Symphony no. 6 “Vincentiana” / Cello Concerto | Einojuhani Rautavaara; Helsinki Philharmonic Orchestra, Max Pommer, Marko Ylönen | | 2 |
| 2000 | Concertos | Nordgren; Marko Ylönen, John‐Edward Kelly, Sören Hermansson, Ostrobothnian Chamber Orchestra, Juha Kangas | | 2 |
| 2000 | Cello Concerto / Seagull Suite | Shchedrin; Marko Ylönen, Helsinki Philharmonic Orchestra, Olli Mustonen | | 1 |
| 2001 | Chamber Works | Astor Piazzolla; Nisinman, Siiskonen, Perelló, Aarnio, Angervo, Ylönen, Tampere Chamber | | 1 |
| 2002 | Duets for the Restless Souls | Pentti Lahti & Marko Ylönen Play Music By László Süle | | 1 |
| 2003 | Complete Piano Trios, Volume 1 | Jean Sibelius; Jaakko Kuusisto, Satu Vänskä, Marko Ylönen, Folke Gräsbeck | | 1 |
| 2004 | Complete Piano Trios, Volume 2 | Jean Sibelius; Jaakko Kuusisto, Marko Ylönen, Folke Gräsbeck | | 1 |
| 2005 | Rock Score for 19 Strings / Cello Concerto no. 1 / Transe-Choral for 15 Strings | Pehr Henrik Nordgren; Marko Ylönen, Ostrobothnian Chamber Orchestra, Juha Kangas | | 1 |
| 2006 | Horn Concerto / Cello Concerto | Jouni Kaipainen; Esa Tapani, Marko Ylönen, Finnish Radio Symphony Orchestra, Hannu Lintu | | 1 |
| 2006 | Symphony no. 3 / Cello Concerto | Pēteris Vasks; Marko Ylönen, Tampere Filharmonia, John Storgårds | | 1 |
| 2007 | Cello Concerto / Symphonies nos. 3 & 4 | Joonas Kokkonen; Marko Ylönen, Finnish Radio Symphony Orchestra, Sakari Oramo | | 1 |
| 2013 | Violin Concerto / Piano Concerto / Phantasy for Cello & Orchestra | Tauno Marttinen; Philippe Graffin, Ralph van Raat, Turku Philharmonic Orchestra, Marko Ylönen, Tampere Philharmonic Orchestra | | 1 |
| 2014 | Poema: Works for Cello and Strings | Salmenhaara, Nordgren, Kangas, Sallinen; Marko Ylönen, Ostrobothnian Chamber Orchestra, Juha Kangas | | 1 |
| 2019 | As in a Dream | Pehr Henrik Nordgren; Marko Ylönen, Lilli Maijala, Olivier Thiery, Ostrobothnian Chamber Orchestra, Juha Kangas | | 2 |
| 2022 | Complete Works for Organ, Volume Three | Axel Ruoff; Jan Lehtola, Marko Ylönen, Petri Komulainen, Darren Acosta, Olli-Pekka Tuomisalo, Annikka Konttori-Gustafsson | | 1 |
| 2023 | Organ Works, Volume One | Marie-Joseph Erb; Paula Malmivaara, Anna-Leena Haikola, Marko Ylönen, Jan Lehtola | | 1 |
| — | Songs: Illalle | Jean Sibelius; Jorma Hynninen, Kalevi Kiviniemi, Laura Hynninen, Marko Ylönen | | 1 |
