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Looking for filler episodes? View the filler guide.
| 4 | Raring to Go | Oct 27, 2004 | Canon |
| 5 | The Shadow Duelist (Part 1) | Nov 3, 2004 | Canon |
| 6 | The Shadow Duelist (Part 2) | Nov 10, 2004 | Canon |
| 7 | Duel and Unusual Punishment | Nov 17, 2004 | Canon |
| 8 | For the Sake of Syrus | Nov 24, 2004 | Canon |
| 9 | Family Business | Dec 1, 2004 | Filler |
| 10 | Tag Team Trial (Part 1) | Dec 7, 2004 | Canon |
| 11 | Tag Team Trial (Part 2) | Dec 14, 2004 | Canon |
| 12 | Formula for Success | Dec 22, 2004 | Canon |
| 13 | Monkey See, Monkey Duel | Dec 29, 2004 | Filler |
| 14 | A Spirit Summoned | Jan 5, 2005 | Filler |
| 15 | Courting Alexis | Jan 12, 2005 | Filler |
| 16 | The Duel Giant | Jan 19, 2005 | Filler |
| 17 | Nature of the Draw | Jan 26, 2005 | Filler |
| 18 | The King of the Copycats (Part 1) | Feb 2, 2005 | Filler |
| 19 | The King of the Copycats (Part 2) | Feb 9, 2005 | Filler |
| 20 | The Maiden in Love | Feb 16, 2005 | Filler |
| 21 | The Duel Off (Part 1) | Feb 23, 2005 | Canon |
| 22 | The Duel Off (Part 2) | Mar 2, 2005 | Canon |
| 23 | The Little Belowski | Mar 9, 2005 | Filler |
| 24 | The New Chazz | Mar 16, 2005 | Canon |
| 25 | The School Duel (Part 1) | Mar 23, 2005 | Canon |
| 26 | The School Duel (Part 2) | Mar 30, 2005 | Canon |
| 27 | Grave Risk (Part 1) | Apr 6, 2005 | Canon |
| 28 | Grave Risk (Part 2) | Apr 13, 2005 | Canon |
| 29 | Doomsday Duel (Part 1) | Apr 20, 2005 | Canon |
| 30 | Doomsday Duel (Part 2) | Apr 27, 2005 | Canon |
| 31 | Field of Screams (Part 1) | May 4, 2005 | Canon |
| 32 | Field of Screams (Part 2) | May 11, 2005 | Canon |
| 33 | Field of Screams (Part 3) | May 18, 2005 | Canon |
| 34 | The Fear Factor | May 25, 2005 | Filler |
| 35 | Sibling Rivalry | Jun 1, 2005 | Filler |
| 36 | Duel Distractions (Part 1) | Jun 8, 2005 | Canon |
| 37 | Duel Distractions (Part 2) | Jun 15, 2005 | Canon |
| 38 | Get Yarr Game On! | Jun 22, 2005 | Filler |
| 39 | The Dark Scorpions | Jun 29, 2005 | Canon |
| 40 | A Lying Legend | Jul 6, 2005 | Canon |
| 41 | A Reason to Win | Jul 13, 2005 | Canon |
| 42 | Duel Monsters Spirit Day | Jul 20, 2005 | Filler |
| 43 | Hearts are Wild | Jul 27, 2005 | Canon |
| 44 | The Seventh Shadow Rider | Aug 3, 2005 | Canon |
| 45 | Amnael's Endgame (Part 1) | Aug 10, 2005 | Canon |
| 46 | Amnael's Endgame (Part 2) | Aug 17, 2005 | Canon |
| 47 | Chazz-anova | Aug 24, 2005 | Filler |
| 48 | Rise of the Sacred Beasts (Part 1) | Aug 31, 2005 | Canon |
| 49 | Rise of the Sacred Beasts (Part 2) | Sep 7, 2005 | Canon |
| 50 | Magna Chum Laude | Sep 14, 2005 | Canon |
| 51 | The Graduation Match (Part 1) | Sep 21, 2005 | Canon |
| 52 | The Graduation Match (Part 2) | Sep 28, 2005 | Canon |
| 53 | Back to Duel | Oct 5, 2005 | Canon |
| 54 | Champion or Chazz-been | Oct 12, 2005 | Filler |
| 55 | A Hassleberry Hounding | Oct 19, 2005 | Canon |
| 56 | Sad but Truesdale | Oct 26, 2005 | Canon |
| 57 | The Demon | Nov 2, 2005 | Canon |
| 58 | A New Breed of Hero (Part 1) | Nov 9, 2005 | Canon |
| 59 | A New Breed of Hero (Part 2) | Nov 16, 2005 | Canon |
| 60 | Pop Goes the Duel | Nov 23, 2005 | Filler |
| 61 | I've Seen the Light | Nov 30, 2005 | Canon |
| 62 | A Greater Porpoise | Dec 7, 2005 | Canon |
| 63 | Curry Worries | Dec 14, 2005 | Filler |
| 64 | Camaraderie Contest | Dec 21, 2005 | Filler |
| 65 | No Pain, No Game | Dec 28, 2005 | Canon |
| 66 | Going Bananas | Jan 4, 2006 | Filler |
| 67 | Homecoming Duel (Part 1) | Jan 11, 2006 | Canon |
| 68 | Homecoming Duel (Part 2) | Jan 18, 2006 | Canon |
| 69 | Dormitory Demolition | Jan 25, 2006 | Canon |
| 70 | Obelisk White? | Feb 1, 2006 | Canon |
| 71 | DuelFellas | Feb 8, 2006 | Filler |
| 72 | Not Playing with a Full Deck | Feb 15, 2006 | Filler |
| 73 | Source of Strength | Feb 22, 2006 | Canon |
| 74 | Happily Never After | Mar 1, 2006 | Filler |
| 75 | Taken by Storm (Part 1) | Mar 8, 2006 | Canon |
| 76 | Taken by Storm (Part 2) | Mar 15, 2006 | Canon |
| 77 | J-Dawg and T-Bone | Mar 22, 2006 | Canon |
| 78 | Mirror, Mirror (Part 1) | Mar 29, 2006 | Canon |
| 79 | Mirror, Mirror (Part 2) | Apr 5, 2006 | Canon |
| 80 | What a Doll! | Apr 12, 2006 | Filler |
| 81 | Let's Make a Duel! | Apr 19, 2006 | Filler |
| 82 | Magnetic Personality | Apr 26, 2006 | Canon |
| 83 | Schooling the Master | May 3, 2006 | Canon |
| 84 | Generation Next | May 10, 2006 | Canon |
| 85 | Rah, Rah, Ra! | May 17, 2006 | Filler |
| 86 | The Art of the Duel | May 24, 2006 | Filler |
| 87 | Blinded by the Light (Part 1) | May 31, 2006 | Canon |
| 88 | Blinded by the Light (Part 2) | Jun 7, 2006 | Canon |
| 89 | The Darkness Within | Jun 14, 2006 | Canon |
| 90 | Pro-Dueling | Jun 21, 2006 | Filler |
| 91 | Don't Fear the Reaper | Jun 28, 2006 | Filler |
| 92 | Duel For Hire | Jul 5, 2006 | Filler |
| 93 | Heart of Ice (Part 1) | Jul 12, 2006 | Canon |
| 94 | Heart of Ice (Part 2) | Jul 19, 2006 | Canon |
| 95 | Tough Love | Jul 26, 2006 | Canon |
| 96 | It's All Relative | Aug 2, 2006 | Canon |
| 97 | The Dark Light | Aug 9, 2006 | Canon |
| 98 | Ultimate Destiny | Aug 16, 2006 | Canon |
| 99 | The Key Factor | Aug 23, 2006 | Canon |
| 100 | The Phoenix Has Landed (Part 1) | Aug 30, 2006 | Canon |