As leader/co-leader

• Searchin' (Naxos, 1997) – rec. 1996
• In the Blink of an Eye (Naxos, 1999)
• Trio (Criss Cross, 1999)
• Mysterious Shorter with Nicholas Payton, Bob Belden, Billy Drummond, John Hart (Chesky, 2006)
• Truth and Beauty (Origin, 2007)
• Jazz Side of the Moon with Ari Hoenig, Mike Moreno, Seamus Blake (Chesky, 2008) – rec. 2007
• Hometown (Posi-Tone, 2009) – rec. 2007
• From Sun to Sun (Origin, 2011)

As a member

Yaya³
With Joshua Redman and Brian Blade

• Yaya³ (Loma, 2002)

As sideman

With Ralph Bowen

• Soul Proprietor (Criss Cross, 2001)
• Five (Criss Cross, 2008) – rec. 2007

With Norah Jones

• Come Away with Me (Blue Note, 2002) – rec. 2000–2001
• Feels Like Home (Blue Note, 2004) – rec. 2003–2004
• Covers (Blue Note, 2012) - compilation

With Ryan Kisor

• 1997: Battle Cry (Criss Cross, 1998)
• 2002: Awakening (Criss Cross, 2003)
• 2002: The Sidewinder (Videoarts, 2003)
• 2003: Donna Lee (Videoarts, 2004)

With Joshua Redman

• Elastic (Warner Bros., 2002)
• Momentum (Nonesuch, 2005)

With Jesse van Ruller

• Circles (Criss Cross, 2003) ^[2]
• Views (Criss Cross, 2006) ^[2]

With others

• Laila Biali, Laila Biali (ACT, 2018)
• Massimo Biolcati, Incontre (Bandcamp, 2020)
• Peter Cincotti, On the Moon (Concord, 2004)
• Larry Coryell, Impressions (Chesky, 2008)
• Charles Davis, Plays the Music of Bent Jaeding (Fresh Sound, 2008)
• Tia Fuller, Diamond Cut (Mack Avenue, 2018)
• Wycliffe Gordon, Dig This! (Criss Cross, 2002)
• Jesper Løvdal, Free Fall (ILK Music, 2008)
• Önder Focan, Beneath The Stars: Yıldızların Altında (Blue Note, 1998)
• Brad Mehldau, Ma Femme Est Une Actrice (Warner, 2001)
• Nicholas Payton, Mysterious Shorter (Chesky, 2006)
• Ben Perowsky, Bop On Pop (JazzKey Music, 2003)
• Madeleine Peyroux, Half the Perfect World (Rounder, 2006)
• Jim Rotondi, New Vistas (Criss Cross, 2004)
• Libor Šmoldas, In New York On Time (Animal Music, 2010)
• Torben Waldorff, Afterburn (Artistshare, 2008)
• Lizz Wright, Salt (Verve, 2003)