| 1980 | Aqua Sansa | Markus Stockhausen & Jasper van ’t Hof | 4 | 3 |
| 1984 | Continuum | Rainer Brüninghaus, Markus Stockhausen, Fredy Studer | | 1 |
| 1987 | Tierkreis / Oberlippentanz | Karlheinz Stockhausen; Suzanne Stephens, Kathinka Pasveer, Markus Stockhausen | | 1 |
| 1989 | Aparis | Markus Stockhausen, Simon Stockhausen & Jo Thönes | | 1 |
| 1989 | Cosi Lontano...Quasi Dentro | Markus Stockhausen / Gary Peacock | | 1 |
| 1993 | Despite the fire-fighters' efforts | Markus Stockhausen, Simon Stockhausen & Jo Thönes | | 1 |
| 1993 | Stockhausen dirigiert KLASSIK: 3 Konzerte: HAYDN (Trompete), MOZART (Flöte – Klarinette) | W. A. Mozart, Joseph Haydn, Karlheinz Stockhausen; Markus Stockhausen, Kathinka Pasveer, Suzanne Stephens | | 2 |
| 1994 | ARIES für Trompete und Elektronische Musik – KLAVIERSTÜCK ⅩⅢ (LUZIFERs TRAUM aus Klaviersolo) | Karlheinz Stockhausen; Markus Stockhausen, Majella Stockhausen-Riegelbauer | | 1 |
| 1994 | Musik für Trompete, Piccolo‐Trompete, Flügelhorn, gespielt von Markus Stockhausen | Karlheinz Stockhausen; Markus Stockhausen | | 1 |
| 1995 | Possible Worlds | Markus Stockhausen | | 1 |
| 1996 | Jubilee | Markus & Simon Stockhausen | | 1 |
| 1996 | Sol Mestizo | Markus Stockhausen | | 1 |
| 2000 | Karta | Markus Stockhausen, Arild Andersen, Patrice Héral & Terje Rypdal | | 1 |
| 2002 | Dedalo | Gianluigi Trovesi, Markus Stockhausen, Fulvio Maras, Tom Rainey, WDR Big Band Köln | | 1 |
| 2003 | ARIES – IN FREUNDSCHAFT – HALT – PIETÀ | Karlheinz Stockhausen; Markus Stockhausen | | 1 |
| 2003 | Bix | Tiger Dixie Band featuring Markus Stockhausen & Lucia Minetti | | 1 |
| 2003 | Gazing Point | Mark Nauseef, Kudsi Ergüner, Markus Stockhausen | | 1 |
| 2003 | Panta rhei | Johannes Tonio Kreusch feat. Markus Stockhausen | | 1 |
| 2004 | Joyosa | Markus Stockhausen • Ferenc Snétberger • Arild Andersen • Patrice Héral | | 1 |
| 2004 | Lichtblick – prima, altrove … | Markus Stockhausen, Angelo Comisso, Christian Thomé | | 1 |
| 2004 | Thinking About | Markus Stockhausen , Tara Bouman | | 1 |
| 2006 | Ergskkem | Gianni Lenoci, Giorgio Dini, Markus Stockhausen | | 1 |
| 2007 | Streams | Ferenc Snétberger & Markus Stockhausen | | 1 |
| 2008 | No Matter | Mark Nauseef / Kudsi Ergüner / Markus Stockhausen / Bill Laswell | | 1 |
| 2009 | Spiral / Pole / Japan / Zyklus / Tierkreis | Stockhausen; Harald Bojé, Christoph Caskel, Péter Eötvös, Tristan Fry, Markus Stockhausen, Margareta Hürholz | 5 | 1 |
| 2010 | Eternal Voyage | Markus Stockhausen, Rabih Lahoud, Dinesh Mishra, Tara Bouman, Florian Weber, Dimitrios Dorian Kokiousis | | 1 |
| 2016 | Alba | Markus Stockhausen, Florian Weber | | 1 |
| 2017 | Far Into the Stars | Markus Stockhausen | | 2 |
| 2020 | Wild Life | Markus Stockhausen | | 1 |
| 2022 | Across Mountains | Markus Stockhausen, Vangelis Katsoulis, Arild Andersen | | 1 |
| 2023 | Content-Blue | Oli Bott, Markus Stockhausen, Oliver Potratz & Eric Schaefer | | 1 |
| — | Abendglühen | Markus Stockhausen | | 1 |
