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Looking for filler episodes? View the filler guide.
| # | Title | Aired | Type |
|---|---|---|---|
| 1 | Awaken! The Best Detective in the World!! | Apr 15, 2003 | Canon |
| 2 | A First Step to Dreams - The Entrance Exam Trap | Apr 22, 2003 | Canon |
| 3 | Final Exam! The Stretched-Around Trap | Apr 29, 2003 | Canon |
| 4 | An Intent to Kill at the School Entrance Ceremony! School Bomb Threat | May 6, 2003 | Canon |
| 5 | Crack the Code!? A Message from the Deceased | May 13, 2003 | Canon |
| 6 | The Perfect 1000-Witness Alibi | May 20, 2003 | Canon |
| 7 | The Jigsaw-Puzzle Will | May 27, 2003 | Canon |
| 8 | The Pretty-Boy Detective! He Appears at Last!! | Jun 3, 2003 | Canon |
| 9 | Showdown! The Cutthroat Who Crossed Through Time!! | Jun 10, 2003 | Canon |
| 10 | The Beautiful Boy Genius - Exposing the Perfect Mystery Room | Jun 17, 2003 | Canon |
| 11 | The Final Deciding Match! The Truth about Q Class!! | Jun 24, 2003 | Canon |
| 12 | A Curse Breaks Out!? The Séance Murder Case | Jul 1, 2003 | Canon |
| 13 | Evil Spirit in the Locked Room! The Unstoppable Murders | Jul 8, 2003 | Canon |
| 14 | An Announcement From the Spiritual World! The Forbidden Truth!! | Jul 15, 2003 | Canon |
| 15 | 30 Meters Underwater. The Case of the Underwater Locked Room Murder | Jul 22, 2003 | Canon |
| 16 | Class Rivalry! Battle of the Vanishing Person | Jul 29, 2003 | Canon |
| 17 | Uncharted Waters that Lead to Death! The Legend of Spirited Away Village | Aug 5, 2003 | Canon |
| 18 | The Conclusive Moment! The Corpse that Disappears into the Sky | Aug 12, 2003 | Canon |
| 19 | The Revelation of Death! You're Next!! | Aug 26, 2003 | Canon |
| 20 | It Comes to Light! The Masked High Priest - Crimes and Lies!! | Sep 2, 2003 | Canon |
| 21 | The Last Mysterious Disappearance! There's Only One Answer | Sep 9, 2003 | Canon |
| 22 | Dinner of the Dead | Oct 4, 2003 | Canon |
| 23 | Train Alibi | Oct 11, 2003 | Canon |
| 24 | The Cursed Idol | Oct 18, 2003 | Canon |
| 25 | An Old Enemy! Pluto | Oct 25, 2003 | Canon |
| 26 | Megumi is Being Targeted | Nov 1, 2003 | Canon |
| 27 | The Lost Dragon | Nov 8, 2003 | Canon |
| 28 | SOS From The Underground Prison | Nov 15, 2003 | Canon |
| 29 | Collector of Killers | Nov 22, 2003 | Canon |
| 30 | Broadcast of the Campus of Death | Nov 29, 2003 | Canon |
| 31 | Tragic on the Net | Dec 6, 2003 | Canon |
| 32 | The Beauties Detective Squad | Dec 13, 2003 | Canon |
| 33 | Mystery of the Home Economics Classroom | Dec 20, 2003 | Canon |
| 34 | The Curse that Disappeared | Dec 27, 2003 | Canon |
| 35 | Bomb of the Terrifying Gem | Jan 10, 2004 | Canon |
| 36 | The Murder Case of the Illusionary House | Jan 17, 2004 | Canon |
| 37 | Rhythm of the Death God | Jan 24, 2004 | Canon |
| 38 | Homicide Concert | Jan 31, 2004 | Canon |
| 39 | The Death March of Friendship | Feb 7, 2004 | Canon |
| 40 | Duel! The Headless Woman | Feb 14, 2004 | Canon |
| 41 | Murder Case of the Maya Princess | Feb 21, 2004 | Canon |
| 42 | Village of the Traitor | Feb 28, 2004 | Canon |
| 43 | Ryu's Determination | Mar 6, 2004 | Canon |
| 44 | Dan Morihiko, Kidnapped! | Mar 13, 2004 | Canon |
| 45 | The Future Detective | Mar 20, 2004 | Canon |