The Main Deck (Japanese: メインのデッキ Mein no Dekki), usually simply referred to as the Deck (デッキ Dekki), is a pile of cards that a Duelist can draw from during play. Each Duelist uses his or her own Main Deck in a Duel.
When constructing a Deck, Monster, Spell and Trap Cards are placed in the Main Deck. Fusion, Synchro, and Xyz Monsters are placed in the Extra Deck. If a player uses official Token Monster cards, these are to be stored in a separate location as well.
When a Duel begins, the Main Deck is placed face-down in the Deck Zone of the Field. All cards in the Main Deck must remain face-down during the Duel (unless a card effect like "Convulsion of Nature" says otherwise). During a Duel, neither player may view the contents of either player's Deck unless a card effect allows them to, after which the Deck must be shuffled. Even if a card in the Deck is face-up, it cannot be looked at by either player unless it is on top of the Deck, in which case it is public knowledge.
Constructed Deck format
The Main Deck must contain only Legal cards.
The Main Deck can have a minimum of 40 cards and a maximum of 60 cards. (Only the cards in the Main Deck, not cards in the Extra Deck, count toward this total.)
A Duelist may not have more than three copies of any Unlimited card included in their Main Deck, Side Deck, and Extra Deck combined.
If a Forbidden, Limited, or Semi-Limited List is used, the number of copies must not exceed those requirements.
Cards which have their name permanently treated as that of another card are considered to be the same as that card for deck construction.
Sealed Deck format
The Main Deck must be constructed using only card product provided at the event.
The Main Deck can have a minimum of 20 cards. There is no maximum size.
A Duelist may include as many copies of any card he or she likes, even more than three.
The Extra Deck (エクストラデッキ, Ekusutoradekki), previously referred to as Fusion Deck (融ゆう合ごうデッキ Yūgō Dekki), is a Deck where Fusion Monsters, Synchro Monsters, and Xyz Monsters, as well as Pendulum Monsters that would otherwise have been sent from the field to the Graveyard, are stored during a Duel. Any old card that still refers to the Fusion Deck applies to the Extra Deck.
The Extra Deck is separate from the Main Deck and is placed face-down in the Extra Deck Zone. Like the Main Deck, the number of cards in the Extra Deck is public knowledge. Unlike the Main Deck, the player that possesses it can look through it at any time. The face-down contents of the Extra Deck are not public knowledge, so the opponent cannot look through face-down cards in the Extra Deck; however, the face-up cards in the Extra Deck are public knowledge, so either player may look through them at any time.
Per the "Maximum of 3 Rule", during Deck construction there can be at most 3 cards with the same name in a player's Main Deck, Extra Deck and Side Deck (combined). During Deck construction, there is a 15-card limit to the Extra Deck, regardless of how many Fusion Monsters, Synchro Monsters, or Xyz Monsters are included. However, Pendulum Monsters placed face-up in the Extra Deck during a Duel can cause the total size of the Extra Deck to be larger than would be allowed during Deck building.
If a Fusion Monster, Synchro Monster, or Xyz Monster would be returned to its owner's hand or Main Deck, it is instead moved to the Extra Deck, since Fusion Monsters, Synchro Monsters, and Xyz Monsters cannot exist in either the hand or the Main Deck. It is not necessary to shuffle the Extra Deck, even when a card specifies that the card is shuffled into the Extra Deck.
A Side Deck (Japanese: サイドデッキ Saidodekki) is a collection of between 1 and 15 cards, separate from the Main Deck. The Side Deck is used in Matches between Duels, to alter the contents of the Main or Extra Deck. Previously, the Side Deck could not be used to alter the contents of the Extra Deck, though this has been changed. This is done to better suit a strategy against an opponent's Deck.
For example, a Burn Deck, a Deck based around dealing direct damage through Card effects and Spell Cards, could be easily countered by including several cards to prevent Life Point damage, such as "Des Wombat" or "Nature's Reflection".
Common Side Deck cards include various forms of Spell and Trap removal, such as "Dust Tornado" and cards that can directly counter common strategies, such as "Prohibition", "Chain Destruction" and "Royal Prison".
Since a Side Deck is not compulsory, a value of 0 for a Side Deck is considered legal. In both the OCG and the TCG, any value between 0 and 15 inclusive is permissible.
The Side Deck is invaluable in tournament play. Facing certain Decks can be a walk in the park or a nightmare depending on the contents of your Side Deck.