| “And the Children Shall Lead”: Gorgon Summoned (M54–60) / Gorgon Zapped (M61) | George Duning / George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 5:13 | |
| “And the Children Shall Lead”: Main Title (soprano version, third season mix) (2006 recording) | George W. Duning, arranged by Alexander Courage, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 1:08 | |
| “And the Children Shall Lead”: Mislead Innocent (M38) / McCoy Mad (M41) / Out of Orbit (M42) / Call the Angel (M43/M43A) | George Duning / George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning | | | 2:58 | |
| “And the Children Shall Lead”: Out of Orbit (alternate) (M42A) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 0:17 | |
| “And the Children Shall Lead”: Standard Orbit #1 (M31) / Starnes’ Tape (M32) / Kids’ Whammy #2 (M33) / Tommy’s Whammy (M34) / Standard Orbit #2 (M35) / Whammed Crew (M36/M36A) / Starnes’ Story (M37) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning / George Duning / George Duning / George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning | | | 5:38 | |
| “And the Children Shall Lead”: Starship Again (M21) / Instant Ice Cream (M22) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning | | | 1:06 | |
| “And the Children Shall Lead”: Triacus (M11) / What Goes Kids? (M12) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning | | | 2:43 | |
| “Balance of Terror”: Theme from Star Trek (9MA part 4) / Romulan Warship (M31) / Romulan Theme (M22A take 3) | Alexander Courage & Gene Roddenberry / Fred Steiner / Fred Steiner | | | 0:57 | |
| “Charlie X”: Goodbye Charlie (M62) / Finale (M63) | Fred Steiner / Fred Steiner & Alexander Courage | | | 1:56 | |
| “Charlie X”: Main Title (cello version) | Alexander Courage & Gene Roddenberry, arranged by Fred Steiner | | | 0:55 | |
| “Charlie X”: Space Orbit (M10) / Charlie X (M11+M11S) / That’s a Girl (M12+M12 chimes) | Alexander Courage / Fred Steiner / Fred Steiner | | | 1:23 | |
| “Is There in Truth No Beauty?”: Ambassador Arrival (alternate) (M13A) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 0:18 | |
| “Is There in Truth No Beauty?”: Ambassador Arrival (M13) / My Life Is Here (M14) / I Must Know (M15) / Starship Party (M21) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Alexander Courage / George Duning, contains "Mr. Spock" by Gerald Fried / George Duning / George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 3:38 | |
| “Is There in Truth No Beauty?”: Don’t Move (M61) / Spock Out (M62) / No Change (M63) / Miranda Mad (M64/M64B/M64A/M64C) / Miranda’s Farewell (M65) | George Duning / George Duning / George Duning / George Duning, contains "Mr. Spock" by Gerald Fried / George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry and "Mr. Spock" by Gerald Fried | | | 7:25 | |
| “Is There in Truth No Beauty?”: Enter Marvick (M11) / Enter Miranda (M12) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning, contains "Mr. Spock" by Gerald Fried | | | 1:39 | |
| “Is There in Truth No Beauty?”: Hero Spock (M53/M53A/M53) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry and "Mr. Spock" by Gerald Fried | | | 3:41 | |
| “Mudd’s Women”: Mudd’s Farewell (M63) / Back in Orbit (M64) | Fred Steiner / Fred Steiner & Alexander Courage | | | 1:27 | |
| “Plato’s Stepchildren”: Brain Bout (M61) | Alexander Courage | | | 1:53 | |
| “Plato’s Stepchildren”: Cut Off / I Hear You Calling (M24/M25+M25A) | Alexander Courage | | | 0:48 | |
| “Plato’s Stepchildren”: Dancing Spock (M33) | Alexander Courage | | | 3:52 | |
| “Plato’s Stepchildren”: Delirium Parmen’s (M15–20) | Alexander Courage | | | 2:36 | |
| “Plato’s Stepchildren”: Episode Titles (M14) | Alexander Courage | | | 0:48 | |
| “Plato’s Stepchildren”: Giant Dwarf (M11) | Alexander Courage | | | 0:47 | |
| “Plato’s Stepchildren”: Groveling Kirk (M32+M32A) | Alexander Courage | | | 2:48 | |
| “Plato’s Stepchildren”: Meet the Folks / Soaring Syringe (M12/M13) | Alexander Courage | | | 1:11 | |
| “Plato’s Stepchildren”: Orgy Porgy (M55–60) | Alexander Courage | | | 6:01 | |
| “Plato’s Stepchildren”: Psychokinetic Shenanigans / Stopped Cold (M26/M31) | Alexander Courage | | | 1:19 | |
| “Plato’s Stepchildren”: Reluctant Guests / Psychokinetic Effect (M21/M21A) | Alexander Courage | | | 0:31 | |
| “Plato’s Stepchildren”: Slap Unhappy (M23) | Alexander Courage | | | 0:43 | |
| “Plato’s Stepchildren”: Spock Brought / New Talent (M41/M51) | Alexander Courage | | | 0:56 | |
| “Plato’s Stepchildren”: The Aristocrats (alternate) (M52A) | Alexander Courage | | | 0:21 | |
| “Plato’s Stepchildren”: The Aristocrats / Flung About (M52/M53) | Alexander Courage | | | 1:26 | |
| “Plato’s Stepchildren”: The Frog (Alexander’s Song) (vocal: Michael Dunn) (M22A) | Alexander Courage | | | 0:29 | |
| “Plato’s Stepchildren”: The Little Visitor (M62) | Alexander Courage | | | 0:44 | |
| “Plato’s Stepchildren”: Tromba Sweetener (alternate) (M25A) | Alexander Courage | | | 0:26 | |
| “Spectre of the Gun”: Final Curtain (alternate) (M63C) | Jerry Fielding, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 0:15 | |
| “The Cage”: Long Look (M45) / Vina’s Punishment (M51) | Alexander Courage | | | 2:05 | |
| “The Cage”: Main Title (M10) | Alexander Courage & Gene Roddenberry | | | 1:01 | |
| “The Cage”: Pike’s Punishment (M52) | Alexander Courage | | | 0:39 | |
| “The Cage”: Prime Specimen (M22–30) / Bottled (M31) | Alexander Courage | | | 5:11 | |
| “The Cage”: Probing (M41) / Monster Illusion (M42) / Monster Fight (M43) / The Kibitzers (M44) | Alexander Courage | | | 5:43 | |
| “The Cage”: Torchy Girl (M63) / Under the Spell (M71) / Primitive Thoughts (M72) | Alexander Courage | | | 1:12 | |
| “The Cage”: Who Was Eve & End Credits (M82) | Alexander Courage & Gene Roddenberry | | | 1:39 | |
| “The Conscience of the King”: Everything Is Later (M51) / Play-Off #3 (M52) | Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 1:54 | |
| “The Conscience of the King”: Kirk and Lenore (M22) / He’s Dead (M23) | Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Joseph Mullendore | | | 1:45 | |
| “The Conscience of the King”: Opheliamania (M62) / Bridge #2 (M63) / Last Cue (M64) | Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 3:08 | |
| “The Conscience of the King”: Play-On #2 (M42) / Quick Ship (M43) / Phaser Overload (M44) | Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Joseph Mullendore | | | 1:41 | |
| “The Conscience of the King”: Ship Play-On (M53) / Woodwind Fanfare (M54) / Reilly Gone (M55) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Joseph Mullendore / Joseph Mullendore | | | 1:12 | |
| “The Conscience of the King”: Spaceship (M24) / 5 Sex and a 1 (M25) / 2 Play-Off #2 (M26) | Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Joseph Mullendore / Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 1:12 | |
| “The Conscience of the King”: Spaceship Play-On (M27) / Toast and Corridor (M31) / Lenore’s Kiss (M32) / Short Bridge (M33) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Joseph Mullendore / Joseph Mullendore | | | 2:33 | |
| “The Conscience of the King”: Spaceship Titles (M13) / Dr. Leighton’s Face (M14) / Bridge #1 (M15) | Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Joseph Mullendore / Joseph Mullendore, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 1:14 | |
| “The Empath”: Empath Finale (M64) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry and "Mr. Spock" by Gerald Fried | | | 1:12 | |
| “The Empath”: How’s It Going (M41) / Spock’s Hypo (M42) / Spock Stuck (M43) / McCoy Tortured (M44) / Gem Wistful (M45) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning / George Duning, contains "Mr. Spock" by Gerald Fried / George Duning / George Duning | | | 3:55 | |
| “The Empath”: Starship Again (M11) / Nova Phase (M12) / What Happened? (M13) | George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / George Duning / George Duning | | | 2:03 | |
| “The Empath”: Vians’ Farewell (M62/M62A) / Off Again (M63) | George Duning / George Duning, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 1:53 | |
| “The Enemy Within”: Alter Ego (M14) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 1:02 | |
| “The Enemy Within”: Another Brandy (M45) / The Evil Grin (M46) / Double Dog Death (M51) | Sol Kaplan / Sol Kaplan / Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 1:27 | |
| “The Enemy Within”: Kirk’s Log (M24) / Indecisive (M31) / Evil Fury (M32) | Sol Kaplan , contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Sol Kaplan / Sol Kaplan | | | 2:50 | |
| “The Enemy Within”: One Captain Kirk (M63) / Thank You, Yeoman (M64) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 1:25 | |
| “The Enemy Within”: Spock Takes Over (M52) / Help Me (M53) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 2:06 | |
| “The Enemy Within”: The Prone Body (M34–41) / Shivering Sulu (M42) / No Repair ( M43) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage, Gene Roddenberry / Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Sol Kaplan | | | 0:39 | |
| “The Enemy Within”: The Rock Slide (M11) / Beam Up (M12) / The Evil Kirk (M13) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage, Gene Roddenberry / Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry / Sol Kaplan | | | 1:13 | |
| “The Enemy Within”: The Tired Captain (M15) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 0:44 | |
| “The Enemy Within”: Two Into One (M62) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 2:21 | |
| “The Enemy Within”: What to Do (M44) | Sol Kaplan, contains "Theme From Star Trek (TV Series)" by Alexander Courage & Gene Roddenberry | | | 0:45 | |
| “The Enterprise Incident”: Aberrated Captain (M11) | Alexander Courage | | | 3:07 | |
| “The Enterprise Incident”: Back from Dead / Commandeered (M42/M43–50) | Alexander Courage | | | 6:34 | |
| “The Enterprise Incident”: Back to Business (M51) | Alexander Courage | | | 2:15 | |
| “The Enterprise Incident”: Ear Bob (M62) | Alexander Courage | | | 0:43 | |
| “The Enterprise Incident”: Free Enterprise (M61) | Alexander Courage | | | 6:22 | |
| “The Enterprise Incident”: Hemmed In / Vulcanization (M22/M31) | Alexander Courage | | | 0:50 | |
| “The Enterprise Incident”: Kirk Rekirked (M41) | Alexander Courage | | | 1:24 | |
| “The Enterprise Incident”: Konked Kirk (M32/M33/M34/M35/M36) | Alexander Courage | | | 3:44 | |
| “The Enterprise Incident”: Main Title (soprano version, monaural; arr. Courage, cond. Hatch) | Alexander Courage | | | 1:06 | |
| “The Enterprise Incident”: Reworked / Deposition / Sweaty Scotty (M53/M54/M55–60) | Alexander Courage | | | 1:52 | |
| “The Enterprise Incident”: Stolen Device (M52) | Alexander Courage | | | 2:53 | |
| “The Enterprise Incident”: Unfair Exchange (alternate) (M14–20A) | Alexander Courage | | | 0:18 | |
| “The Enterprise Incident”: Unfair Exchange (M14–20+M14–20B) | Alexander Courage | | | 1:05 | |
| “The Enterprise Incident”: Vulcanian Cahoots (M21) | Alexander Courage | | | 3:36 | |
| “The Enterprise Incident”: Vulcanized (M33) | Alexander Courage | | | 1:16 | |
| “The Man Trap”: At First Sight (M34) / Pill Tosser (M35–41) | Alexander Courage | | | 2:54 | |
| “The Man Trap”: Circle One (M24) / Monitor Gizzard (M25) / Down Again (M26) / Grey to Greene (M31) | Alexander Courage | | | 3:18 | |
| “The Man Trap”: Conference (M53) | Alexander Courage | | | 4:50 | |
| “The Man Trap”: Dead Crater (M54) / Last of the Last (M61) | Alexander Courage | | | 4:16 | |
| “The Man Trap”: Episode Titles (M12) / Genuine Affection (M13) | Alexander Courage | | | 1:01 | |
| “The Man Trap”: First Goner (M14–21) / Salty Cat (M22) / Dressing Down (M23) | Alexander Courage | | | 1:54 | |
| “The Man Trap”: Main Title (electric violin version) | Alexander Courage & Gene Roddenberry | | | 0:55 | |
| “The Man Trap”: Nancy Schmancy (M42) | Alexander Courage | | | 1:56 | |
| “The Man Trap”: Noisy Plant (M33) | Alexander Courage | | | 1:08 | |
| “The Man Trap”: Salt Chaser (M32) | Alexander Courage | | | 1:35 | |
| “The Man Trap”: Small Planet Visit (M10) / The Changeling (M11) | Alexander Courage | | | 3:29 | |
| “The Man Trap”: The Unreal McCoy (M43) | Alexander Courage | | | 2:03 | |
| “The Man Trap”: Top Security (M44) / Lazer Dazer (M45–51) / Dodo Girl (M52) | Alexander Courage | | | 4:05 | |
| “The Man Trap”: Trailer (“The Man Trap”) | Alexander Courage | | | 1:09 | |
| “The Man Trap”: Warp One (M62) | Alexander Courage & Gene Roddenberry | | | 0:48 | |
| “The Naked Time”: Brass Monkeys (M10) / Out of Glove (M11) | Alexander Courage & Gene Roddenberry / Alexander Courage | | | 3:00 | |
| “The Naked Time”: Breaking Planet (M12) / Sweaty Palm (M13) / Itchy Hand (M14) | Alexander Courage & Gene Roddenberry / Alexander Courage / Alexander Courage | | | 1:23 | |
| “The Naked Time”: Captain’s Wig (M54–61) | Alexander Courage | | | 4:02 | |
| “The Naked Time”: End Title (electric violin version) | Alexander Courage & Gene Roddenberry | | | 0:46 | |
| “The Naked Time”: Party Time (M44) | Alexander Courage | | | 1:36 | |
