| Title | Year | Album | Lyricist | Length | Notes | | "2285 Entr'acte" | 2016 | The Astonishing | Instrumental | 2:20 |
| "6:00" | 1994 | Awake | Kevin Moore | 5:31 |
| "A Better Life" | 2016 | The Astonishing | John Petrucci | 4:39 |
| "A Change of Seasons" | 1995 | A Change of Seasons | Mike Portnoy | 23:09 | Originally written in 1989 and supposed to appear on Images and Words, but cut due to the album being already too long. The song was re-worked and released on the EP A Change of Seasons. The original version was never officially released. |
| "A Crack in the Mirror" | 1994 | {{N/A}} | Instrumental | 1:05 | Extended intro added to "The Mirror". Only played live during the Waking Up the World Tour (1994-95) and never officially released. |
| "A Fortune in Lies" | 1989 | When Dream and Day Unite | John Petrucci | 5:12 |
| "A Life Left Behind" | 2016 | The Astonishing | John Petrucci | 5:49 |
| "A Mind Beside Itself: I. Erotomania" | 1994 | Awake | Instrumental | 6:44 |
| "A Mind Beside Itself: II. Voices" | 1994 | Awake | John Petrucci | 9:53 |
| "A Mind Beside Itself: III. The Silent Man" | 1994 | Awake | John Petrucci | 3:47 | Released as a single. A music video was made for the song. |
| "A New Beginning" | 2016 | The Astonishing | John Petrucci | 7:40 |
| "A Nightmare to Remember" | 2009 | Black Clouds & Silver Linings | John Petrucci | 16:10 |
| "A Rite of Passage" | 2009 | Black Clouds & Silver Linings | John Petrucci | 8:36 | Released as a single. A music video was made for the song. |
| "A Savior in the Square" | 2016 | The Astonishing | John Petrucci | 4:13 |
| "A Tempting Offer" | 2016 | The Astonishing | John Petrucci | 4:19 |
| "A Vision" | 1986 | Majesty Demos | Kevin Moore | 11:24 | Two versions exist for this song:- The original version released on The Majesty Demos (11:24).
- A reworked version with Charlie Dominici on vocals. It appears on the When Dream and Day Unite Demos released as "A Vision 89" (7:10).
|
| "Act of Faythe" | 2016 | The Astonishing | John Petrucci | 5:00 |
| "Afterlife" | 1989 | When Dream and Day Unite | Charlie Dominici | 5:26 | A remixed version was released as a promo single. This song was written while Chris Collins was in the band and originally featured his lyrics and a different vocal melody, although the song title was the same. |
| "Along for the Ride" | 2013 | Dream Theater | John Petrucci | 4:45 | Released as a single. |
| "Anna Lee" | 1997 | Falling Into Infinity | James LaBrie | 5:51 |
| "Another Day" | 1992 | Images and Words | John Petrucci | 4:23 | Released as a single. A music video was made for the song. |
| "Another Hand" | 1993 | Live at the Marquee | Instrumental | 2:12 | Instrumental that connected "Another Day" and "The Killing Hand" when performed live in 1992 and 1993. Also was used as the intro to "The Killing Hand" on later tours. |
| "Another Won" | 1986 | Majesty Demos | John Petrucci | 5:27 | Appears on the Score live album. |
| "As I Am" | 2003 | Train of Thought | John Petrucci | 7:47 | Released as a single. |
| "Astonishing" | 2016 | The Astonishing | John Petrucci | 5:51 |
| "At Wit's End" | 2019 | Distance over Time | James LaBrie | 9:20 |
| "Awake Jam" | 1994 | {{N/A}} | Instrumental | 5:39 | Improvisation jam. Only played live during the Waking Up the World Tour (1994-95) and never officially released. |
| "Barfbag" | 1993 | {{N/A}} | Instrumental | {{N/A}} | Improvisation jam. Only played live in the autumn of 1993 and never officially released. |
| "Barstool Warrior" | 2019 | Distance over Time | John Petrucci | 6:43 |
| "Begin Again" | 2016 | The Astonishing | John Petrucci | 3:54 |
| "Behind the Veil" | 2013 | Dream Theater | John Petrucci | 6:52 |
| "Beneath the Surface" | 2011 | A Dramatic Turn of Events | John Petrucci | 5:26 |
| "Blind Faith" | 2002 | Six Degrees of Inner Turbulence | James LaBrie | 10:21 |
| "Bombay Vindaloo" | 1993 | Live at the Marquee | Instrumental | 6:48 | Improvisation jam. Only played live. |
| "Breaking All Illusions" | 2011 | A Dramatic Turn of Events | John Myung and John Petrucci | 12:25 |
| "Bridges in the Sky" | 2011 | A Dramatic Turn of Events | John Petrucci | 11:01 |
| "Brother, Can You Hear Me?" | 2016 | The Astonishing | John Petrucci | 5:11 |
| "Build Me Up, Break Me Down" | 2011 | A Dramatic Turn of Events | John Petrucci | 6:59 | Released as a single. |
| "Burning My Soul" | 1997 | Falling into Infinity | Mike Portnoy | 5:29 | The original demo version is 9 minutes long and included a mellow introduction and most of what became Hell's Kitchen. |
| "Caught in a Web" | 1994 | Awake | James LaBrie and John Petrucci | 5:28 | Released as a promo single. |
| "Chosen" | 2016 | The Astonishing | John Petrucci | 4:32 |
| "Constant Motion" | 2007 | Systematic Chaos | Mike Portnoy | 6:55 | Released as a single. A music video was made for this song. |
| "Cover My Eyes" | 1997 | Falling into Infinity Demos | John Petrucci | 3:23 | Cut from the final album. A live acoustic version appears on Once in a LIVEtime. |
| "Cry for Freedom" | 1986 | When Dream and Day Unite Demos | Chris Collins | 6:46 | While this song had lyrics, and the song was performed live with Chris, the only "proper" recordings of this song that exist are instrumental demos. |
| "Descent of the NOMACS" | 2016 | The Astonishing | NOMACS Instrumental | 1:10 |
| "Digital Discord" | 2016 | The Astonishing | NOMACS Instrumental | 0:47 |
| "Disappear" | 2002 | Six Degrees of Inner Turbulence | James LaBrie | 6:46 |
| "Don't Look Past Me" | 1992 | Images and Words Demos | Kevin Moore | 6:25 | Cut from the final album. Never officially released. James LaBrie re-recorded vocals for this song in 1999 which were added to the original 1990 demo for a fanclub CD release. |
| "Dystopian Overture" | 2016 | The Astonishing | Instrumental | 4:50 |
| "Endless Sacrifice" | 2003 | Train of Thought | John Petrucci | 11:24 |
| "Enigma Machine" | 2013 | Dream Theater | Instrumental | 6:01 |
| "Eve" | 1992 | The Silent Man | Instrumental | 5:10 | Initially performed live in 1993. Recorded during the Awake sessions but cut from the final album. Appears as a B-side on The Silent Man single. |
| "Fall into the Light" | 2019 | Distance over Time | John Myung and John Petrucci | 7:04 | Second single for Distance over Time |
| "False Awakening Suite" | 2013 | Dream Theater | Instrumental | 2:42 |
| "Far from Heaven" | 2011 | A Dramatic Turn of Events | James LaBrie | 3:56 |
| "Forsaken" | 2007 | Systematic Chaos | John Petrucci | 5:35 | Released as a single. A music video was made for the song. |
| "Heaven's Cove" | 2016 | The Astonishing | John Petrucci | 4:19 |
| "Hell's Kitchen" | 1997 | Falling into Infinity | Instrumental | 4:16 | Most of this song was originally an instrumental part of "Burning My Soul". |
| "Hollow Years" | 1997 | Falling into Infinity | John Petrucci | 5:53 | Released as a single. A music video was made for the song |
| "Honor Thy Father" | 2003 | Train of Thought | Mike Portnoy | 10:14 |
| "Hymn of a Thousand Voices" | 2016 | The Astonishing | John Petrucci | 3:38 |
| "I Walk Beside You" | 2005 | Octavarium | John Petrucci | 4:29 |
| "Illumination Theory" | 2013 | Dream Theater | John Petrucci | 22:17 |
| "In the Name of God" | 2003 | Train of Thought | John Petrucci | 14:16 |
| "In the Presence of Enemies" | 2007 | Systematic Chaos | John Petrucci | 25:38 (full song)
9:00 (part 1)
16:38 (part 2)
| Split in two parts on the Systematic Chaos album. |
| "Innocence Faded" | 1994 | Awake | John Petrucci | 5:42 |
| "Just Let Me Breathe" | 1997 | Falling into Infinity | Mike Portnoy | 5:28 |
| "Learning to Live" | 1992 | Images and Words | John Myung | 11:30 |
| "Lie" | 1994 | Awake | Kevin Moore | 6:33 | A music video was made for the song |
| "Lifting Shadows Off a Dream" | 1994 | Awake | John Myung | 6:05 |
| "Light Fuse and Get Away" | 1989 | When Dream and Day Unite | Kevin Moore | 7:23 |
| "Lines in the Sand" | 1997 | Falling into Infinity | John Petrucci | 12:05 |
| "Lord Nafaryus" | 2016 | The Astonishing | John Petrucci | 3:28 |
| "Losing Faythe" | 2016 | The Astonishing | John Petrucci | 4:13 |
| "Lost Not Forgotten" | 2011 | A Dramatic Turn of Events | John Petrucci | 10:11 |
| "Machine Chatter" | 2016 | The Astonishing | NOMACS Instrumental | 1:03 |
| "March of the Tyrant" | 1986 | Majesty Demos | John Myung | 5:34 |
| "Metropolis Pt. I: The Miracle and the Sleeper" | 1992 | Images and Words | John Petrucci | 9:32 |
| "Metropolis Pt. II" | 1996 | Falling into Infinity Demos | Instrumental (lyrics never written) | 21:25 | Original epic sequel to Metropolis pt. I and intended for the Falling into Infinity album. Lyrics were never written and this version of the song was abandoned once they decided to expand it into a full album, which became Scenes from a Memory |
| "Misunderstood" | 2002 | Six Degrees of Inner Turbulence | John Petrucci | 9:32 |
| "Moment of Betrayal" | 2016 | The Astonishing | John Petrucci | 6:11 | Released as a promo single. |
| "Moon Bubbles" | 1992 | {{N/A}} | Instrumental | {{N/A}} | Improvisation jam on guitar and bass. Only played live and never officially released. |
| "My Last Farewell" | 2016 | The Astonishing | John Petrucci | 3:44 |
| "Never Enough" | 2005 | Octavarium | Mike Portnoy | 6:46 |
| "New Millennium" | 1997 | Falling into Infinity | Mike Portnoy | 8:20 |
| "Octavarium" | 2005 | Octavarium | James LaBrie, John Petrucci, and Mike Portnoy | 24:00 |
| "Only a Matter of Time" | 1989 | When Dream and Day Unite | Kevin Moore | 6:35 |
| "On the Backs of Angels" | 2011 | A Dramatic Turn of Events | John Petrucci | 8:42 | Released as a single. A music video was made for the song. |
| "Our New World" | 2016 | The Astonishing | John Petrucci | 4:12 | Featuring Lizzy Hale on vocals. Released as a promo single. A music video was made for the song. |
| "Out of Reach" | 2019 | Distance over Time | James LaBrie | 4:04 |
| "Outcry" | 2011 | A Dramatic Turn of Events | John Petrucci | 11:24 |
| "Pale Blue Dot" | 2019 | Distance over Time | John Petrucci | 8:25 |
| "Panic Attack" | 2005 | Octavarium | John Petrucci | 8:13 |
| "Paralyzed" | 2019 | Distance over Time | John Petrucci | 4:17 | Third single for Distance over Time |
| "Peruvian Skies" | 1997 | Falling into Infinity | John Petrucci | 6:43 |
| "Power Down" | 2016 | The Astonishing | NOMACS Instrumental | 1:25 |
| "Prophets of War" | 2007 | Systematic Chaos | James LaBrie | 6:00 |
| "Pull Me Under" | 1992 | Images and Words | Kevin Moore | 8:14 | Released as a promo single. A music video was made for the song. |
| "Puppies on Acid" | 1994 | Awake sessions | Instrumental | 1:24 | Intro part of "The Mirror", and also the working title of this song. Appears on Once in a LIVEtime |
| "Raise the Knife" | 1997 | Falling into Infinity Demos, Score | Mike Portnoy | 11:40 | Cut from the final album. A live version appears on the Score live album. |
| "Ravenskill" | 2016 | The Astonishing | John Petrucci | 6:01 |
| "Raw Dog" | 2010 | Blood & Metal | Instrumental | 7:33 | Last song to be recorded with Mike Portnoy. |
| "Repentance" | 2007 | Systematic Chaos | Mike Portnoy | 10:43 | Part four of the Twelve-step Suite. |
| "Room 137" | 2019 | Distance over Time | Mike Mangini | 4:23 |
| "S2N" | 2019 | Distance over Time | John Myung and John Petrucci | 6:21 |
| "Sacrificed Sons" | 2005 | Octavarium | James LaBrie | 10:42 |
| "Scarred" | 1994 | Awake | John Petrucci | 10:59 |
| "Scene Eight: The Spirit Carries On" | 1999 | Scenes from a Memory | John Petrucci | 6:38 |
| "Scene Five: Through Her Eyes" | 1999 | Scenes from a Memory | John Petrucci | 5:29 | Released as a single. |
| "Scene Four: Beyond This Life" | 1999 | Scenes from a Memory | John Petrucci | 11:22 |
| "Scene Nine: Finally Free | 1999 | Scenes from a Memory | Mike Portnoy | 11:59 |
| "Scene One: Regression" | 1999 | Scenes from a Memory | John Petrucci | 2:06 |
| "Scene Seven: I. The Dance of Eternity" | 1999 | Scenes from a Memory | Instrumental | 6:13 |
| "Scene Seven: II. One Last Time" | 1999 | Scenes from a Memory | James LaBrie | 3:46 |
| "Scene Six: Home" | 1999 | Scenes from a Memory | Mike Portnoy | 12:53 | Released as a promo single. |
| "Scene Three: I. Through My Words | 1999 | Scenes from a Memory | John Petrucci | 1:02 |
| "Scene Three: II. Fatal Tragedy" | 1999 | Scenes from a Memory | John Myung | 6:49 |
| "Scene Two: I. Overture 1928" | 1999 | Scenes from a Memory | Instrumental | 3:37 |
| "Scene Two: II. Strange Deja Vu" | 1999 | Scenes from a Memory | Mike Portnoy | 5:12 |
| "Six Degrees of Inner Turbulence" | 2002 | Six Degrees of Inner Turbulence | John Petrucci and Mike Portnoy | 42:02 | Divided into eight parts :- "I. Overture" (6:50)
- "II. About to Crash" (5:50)
- "III. War Inside My Head" (2:08)
- "IV. The Test That Stumped Them All" (5:03)
- "V. Goodnight Kiss" (6:17)
- "VI. Solitary Shell" (5:47)
- "VII. About to Crash (Reprise)" (4:04)
- "VIII. Losing Time/Grand Finale" (5:59)
|
| "Slow Motion" | 1993 | {{N/A}} | Instrumental | {{N/A}} | Improvisation jam. Only played live in January 1993 and never officially released. |
| "Space-Dye Vest" | 1994 | Awake | Kevin Moore | 7:29 |
| "Speak to Me" | 1997 | Falling into Infinity Demos | James LaBrie | 6:25 | 6' MINI CD. Appears on Falling Into Infinity - Japanese version - EastWest Records America – AMCY-2315-S |
| "Status Seeker" | 1989 | When Dream and Day Unite | Charlie Dominici and John Petrucci | 4:17 | A remixed version was released as a promo single. |
| "Stream of Consciousness" | 2003 | Train of Thought | Instrumental | 11:16 |
| "Surrender to Reason" | 2013 | Dream Theater | John Myung | 6:34 |
| "Surrounded" | 1992 | Images and Words | Kevin Moore | 5:30 |
| "Take Away My Pain" | 1997 | Falling into Infinity | John Petrucci | 6:03 |
| "Take the Time" | 1992 | Images and Words | John Petrucci, Mike Portnoy, John Myung and Kevin Moore [1] | 8:21 | Released as a promo single. A music video was made for the song. |
| "The Answer" | 2016 | The Astonishing | John Petrucci | 1:52 |
| "The Answer Lies Within" | 2005 | Octavarium | John Petrucci | 5:33 |
| "The Best of Times" | 2009 | Black Clouds & Silver Linings | Mike Portnoy | 13:09 |
| "The Bigger Picture" | 2013 | Dream Theater | John Petrucci | 7:40 | Released as a single. |
| "The Count of Tuscany" | 2009 | Black Clouds & Silver Linings | John Petrucci | 19:16 |
| "The Dark Eternal Night" | 2007 | Systematic Chaos | John Petrucci | 8:53 |
| "The Enemy Inside" | 2013 | Dream Theater | John Petrucci | 6:17 | Released as a single. A music video was made for the song. |
| "The Gift of Music" | 2016 | The Astonishing | John Petrucci | 4:00 | Released as a promo single. A music video was made for the song. |
| "The Glass Prison" | 2002 | Six Degrees of Inner Turbulence | Mike Portnoy | 13:53 | Part one of the Twelve-step Suite. |
| "The Great Debate" | 2002 | Six Degrees of Inner Turbulence | John Petrucci | 13:46 |
| "The Hovering Sojourn" | 2016 | The Astonishing | NOMACS Instrumental | 0:27 |
| "The Killing Hand" | 1989 | When Dream and Day Unite | John Petrucci | 8:41 |
| "The Looking Glass" | 2013 | Dream Theater | John Petrucci | 4:53 | Released as a single. A music video was made for the song. |
| "The Ministry of Lost Souls" | 2007 | Systematic Chaos | John Petrucci | 14:57 |
| "The Mirror" | 1994 | Awake | Mike Portnoy | 6:45 |
| "The Path That Divides" | 2016 | The Astonishing | John Petrucci | 5:09 |
| "The Ones Who Help to Set the Sun" | 1989 | When Dream and Day Unite | John Petrucci | 8:05 |
| "The Road to Revolution" | 2016 | The Astonishing | John Petrucci | 3:35 |
| "The Root of All Evil" | 2005 | Octavarium | Mike Portnoy | 8:25 | Part three of the Twelve-step Suite. |
| "The Shattered Fortress" | 2009 | Black Clouds & Silver Linings | Mike Portnoy | 12:49 | Part five of the Twelve-step Suite. |
| "The Walking Shadow" | 2016 | The Astonishing | John Petrucci | 2:58 |
| "The Way It Used to Be" | 1997 | Hollow Years, Falling Into Infinity Demos | James LaBrie | 7:47 | Cut from the final album. Appears on the Hollow Years single. |
| "The X Aspect" | 2016 | The Astonishing | John Petrucci | 4:13 |
| "These Walls" | 2005 | Octavarium | John Petrucci | 7:36 |
| "This Dying Soul" | 2003 | Train of Thought | Mike Portnoy | 11:27 | Part two of the Twelve-step Suite. |
| "This Is the Life" | 2011 | A Dramatic Turn of Events | John Petrucci | 6:57 |
| "Three Days" | 2016 | The Astonishing | John Petrucci | 3:44 |
| "To Live Forever" | 1992 | Lie, Greatest Hit (...and 21 Other Pretty Cool Songs), Images and Words Demos | John Petrucci, Kevin Moore | 4:26 | Originally written in 1987. 4 versions exist :- A demo from 1988 with Charlie Dominici singing. Never officially released.
- A demo recorded in 1990. Separate versions featuring the vocals of John Hendricks and Steve Stone (with the same backing track) were released on the Images and Words Demos official bootleg.
- A high quality demo recorded before the Images and Words sessions in 1991. Released on the Images and Words Demos official bootleg.
- A version recorded during the Awake sessions. Appears on the Lie single and on the Greatest Hit (...and 21 Other Pretty Cool Songs) compilation album.
|
| "Trial of Tears" | 1997 | Falling into Infinity | John Myung | 13:06 |
| "Two Far" | 1986 | Majesty Demos | Kevin Moore | 5:25 |
| "Under a Glass Moon" | 1992 | Images and Words | John Petrucci | 7:03 |
| "Untethered Angel" | 2019 | Distance over Time | John Petrucci | 6:14 | First single for Distance over Time |
| "Vacant" | 2003 | Train of Thought | James LaBrie | 2:57 |
| "Viper King" | 2019 | Distance over Time | James LaBrie | 4:00 |
| "Vital Star" | 1986 | Majesty Demos | Kevin Moore | 5:44 |
| "Wait for Sleep" | 1992 | Images and Words | Kevin Moore | 2:31 |
| "When Your Time Has Come" | 2016 | The Astonishing | John Petrucci | 4:19 |
| "Where Are You Now" | 1997 | Falling into Infinity Demos | John Petrucci | 7:27 | Cut from the final album. Never officially released. |
| "Whispers on the Wind" | 2016 | The Astonishing | John Petrucci | 1:37 |
| "Wither" | 2009 | Black Clouds & Silver Linings | John Petrucci | 5:25 | Released as the Wither EP. A music video was made for the song. A version with John Petrucci singing (with the same album backing track) also exists, as does a completely separate version on piano and vocals only. |
| "You Not Me" | 1997 | Falling into Infinity | John Petrucci and Desmond Child | 4:58 | Heavily re-worked version of "You Or Me". |
| "You Or Me" | 1997 | Hollow Years, Falling Into Infinity sessions | John Petrucci | 6:28 | Original version of "You Not Me". Appears on the Hollow Years single. |
| "Your Majesty" | 1986 | Majesty Demos | John Petrucci | 3:45 |
| "Ytse Jam" | 1989 | When Dream and Day Unite | Instrumental | 5:46 |
| Title | Appearances | Notes | | "Caught in a New Millennium" | Live Scenes from New York | Mashup of "Caught in a Web" and "New Millennium". Played in 2000 during the Metropolis 2000 tour. |
| "Caught in Alice's Nine-Inch Tool Garden" | Old Bridge, New Jersey – 12/14/96 (CD) official bootleg | Not a true medley, but rather a reworked version of "Caught in a Web", influenced by Alice in Chains, Nine Inch Nails, Tool and Soundgarden. Played around December 1996, and April & September 1997. Served as the initial basis for what later became the song "New Millennium" |
| Unnamed medley, labeled by fans as "Falling Into a Change of Awake" | {{N/A}} | Selections from the tracks "Puppies on Acid", "A Change of Seasons", "Just Let Me Breathe", Liquid Tension Experiment's "Acid Rain", "Caught in a Web" and "New Millenium". Played in 2000 during the Metropolis 2000 tour. |
| "Instrumedley" | Live at Budokan | Selections from the tracks "The Dance of Eternity", "Metropolis Pt. 1: The Miracle and the Sleeper", "Erotomania", "A Change of Seasons", "Ytse Jam" and songs by Liquid Tension Experiment. Played during the World Tourbulence and Train of Thought tours. |
| "Schmedley Wilcox" | Chaos in Motion 2007-2008 | Selections from the tracks "Trial of Tears", "Finally Free", "Learning to Live", "In the Name of God" and "Octavarium". Played as an encore song for most of the shows of the Chaos in Motion tour. |
| "The Big Medley" | A Change of Seasons | Mashup of the following covers :- In the Flesh? (Pink Floyd)
- Carry On Wayward Son (Kansas)
- Bohemian Rhapsody (Queen)
- Lovin', Touchin', Squeezin' (Journey)
- Cruise Control (Dixie Dregs)
- Turn it on Again (Genesis)
Played only at the uncovered fan club gig at the Ronnie Scott's Jazz Club in London (England), on January 31, 1995. |
| "When Images and Words Unite" | Through Her Eyes single | Selection from the tracks "Pull Me Under", "Under a Glass Moon", "A Fortune in Lies", "Only a Matter of Time" and "Take the Time". Played during the Scenes from a Memory and Metropolis 2000 tours. |
1. ^{{cite web|last=Portnoy|first=Mike|title=MP Twitter Q&A - The Official Mike Portnoy Forums|url=http://www.mikeportnoy.com/forum/m2811186.aspx|accessdate=20 January 2013}}
{{Dream Theater}}