| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Head in the Clouds (2) | 3 | 112 | Saturday June 23, 2007 |
| Heart of Ice (1) | 2 | 93 | Wednesday February 7, 2007 |
| Heart of Ice (2) | 2 | 94 | Thursday February 8, 2007 |
| Hearts Are Wild | 1 | 43 | Friday March 3, 2006 |
| Homecoming Duel (1) | 2 | 67 | Monday October 2, 2006 |
| Homecoming Duel (2) | 2 | 68 | Tuesday October 3, 2006 |
| I've Seen the Light | 2 | 61 | Thursday August 31, 2006 |
| Inter-Dimension Detention | 3 | 120 | Saturday September 22, 2007 |
| It's All Relative | 2 | 96 | Monday February 12, 2007 |
| J-Dawg and T-Bone | 2 | 77 | Tuesday October 17, 2006 |
| Jaden Revived!? A Brand New Journey! | 3 | 156 | |
| Jaden vs Alexis: Face-Down Card of Hidden Emotion | 4 | 162 | |
| Jewel of A Duel (1) | 3 | 106 | Saturday April 14, 2007 |
| Jewel of A Duel (2) | 3 | 107 | Saturday April 21, 2007 |
| Let's Make a Duel | 2 | 81 | Saturday November 18, 2006 |
| Magna Chum Laude | 1 | 50 | Tuesday April 4, 2006 |
| Magnetic Personality | 2 | 82 | Saturday December 2, 2006 |
| Making the Grade | 1 | 4 | Thursday October 13, 2005 |
| Mirror, Mirror (1) | 2 | 78 | Saturday October 28, 2006 |
| Mirror, Mirror (2) | 2 | 79 | Saturday November 4, 2006 |
| Monkey See, Monkey Duel | 1 | 13 | Thursday October 27, 2005 |
| Nature of the Draw | 1 | 17 | Wednesday November 16, 2005 |
| Neos VS The Advanced Crystal Beasts | 3 | 151 | |
| Night of the Living Duelist | 3 | 122 | Saturday October 6, 2007 |
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