We won't discuss penalties for Illegal Deck and Illegal Decklist here, although we'll cover what's legal and illegal. We're going to focus on the mechanics of the deck check. If at any time during the process you discover a discrepancy, consult the Penalty Guidelines for the appropriate actions. Especially with actions that involve counting, have someone double-check your math. A second (or third) set of eyes never hurts.
Most of what we'll discuss below applies to both Constructed and Limited events. I'll make special note when it applies to only one.
The Deck List
Once you collect them, the first order of business is sorting the decklists. Sorting lets you easily find lists later in the tournament. If you have the luxury, this can be handled by non-Judging staff. Sort alphabetically by last name. If you have identical names (which may happen at larger tournaments), make sure that you can differentiate between the individuals. Work with the scorekeeper on this as well. At larger tournaments, especially if you're short on staff, simply sorting the lists can take the entire first round.
If you're having a large Limited tournament, set up multiple land stations. Have the players turn in their decklists when they come get their lands or do their land swap. Let the players take their own lands while you give the decklist a cursory glance. Ensure it has the necessary elements: name and DCI number. Have another staff member floating between the land stations, collecting the lists and taking them to another staff member, who sorts them on the fly.
The next thing to do with the decklists is check them for legality. Again, if you are fortunate to have sufficient staff, this can be handled by non-Judges, although it should be done by someone familiar with the game and the format. This can be done while rounds are being played. Ideally, the deck list should be checked well before a player gets deck checked, limiting the amount of time taken away from the tournament.
Check first for the minimum number of cards (60 in Constructed, 40 in Limited) and a legal sideboard (15 or 0 in Constructed; Limited is dependent on the format). Then ensure all cards listed are legal for the format. Finally, see if the list contains cards that would violate a game rule, like the 4-card limit or more than 1 of a restricted card.
When doing a count in a Limited tournament, especially once with multiple deck sheets, I like to put a total number of cards at the bottom of each column. This way, you can get a quick card total at the end.
Once everything is counted and legal the list is ready and waiting for the deck to be checked.
Determining Which Decks are Checked
How many checks you do is dependent on your staffing level. Obviously, the more people you can dedicate to the effort, the greater your assurance factor becomes. At Pro Tour-level events, we check 4-6 decks every round, taking both decks from 2-3 tables. Checking both decks at a single table reduces the time taken away from the tournament.
For the most part, determine randomly by table number which decks you're going to check. A relatively objective source, like the scorekeeper, can choose the numbers. In later rounds of tournaments, some organizers like to focus their checks on the tables still in contention. If you have reasonable cause to be suspicious of a particular deck (like a legal but somehow spurious decklist), feel free to do a targeted check. Be careful about doing this; don't develop a habit of picking on players, regardless of reputation.
Don't be afraid to check the same player twice in a single event. It lets players know that they're never sure when they're going to be checked. At Premier Events, don't hesitate to check players at Feature Matches. No one is above the law.
Checking the Deck: Preparation
The Head Judge will assign Judges to check specific tables. Whether it's one Judge or two checking both players at that table, position yourself at a discreet distance from the table. Wait for the players to present their decks to each other before notifying the players that they're being checked. The presentation is the point that the game begins in earnest.
Take the decks away from the playing area to do the check. You don't want to risk a competitor accidentally seeing a card. If you have the time, get the decklist beforehand and have it there waiting. Now you're ready to do the check. The checks themselves should be done by Judges or experienced staff.
Checking the Deck: the sleeves
Before you look at the face of the cards, check the sleeves if they're opaque, the sleeves and the backs of the cards if the sleeves are clear, or the backs if the deck is unsleeved. Look for obvious patterns of marks or uneven wear. Uneven wear also means that there is some marking that's different on numerous cards. Check for bends, creases, or broken sleeves.
Be discerning but reasonable. Some wear is inevitable; if they're all equally-worn, they're okay. The only time wear is a concern is when some are well-worn and some aren't. If this is the case, then you have a case of Marked Cards.
Now comes the tricky part. Once you find some marked cards, determine whether or not there's a pattern. This is the first time you'll look at the face of the cards. Marked Cards-No Pattern means there's no reasonable relationship between the cards. Again, you'll have to use some discretion; this is where experience comes in. Here are some examples of No Pattern:
There are four marked cards: An Island, a Dismantling Blow, a Voice of All, and a Plains.
Marked Cards-Observable Pattern is a more serious issue. Here are some examples:
Four Wrath of God are new or in new sleeves; the rest of the cards are worn or in worn sleeves.
Cards are also marked if they're facing a different direction in the deck than the rest of the cards-sleeved or not. Unsleeved/clear-sleeved is easier to see, but even in opaque sleeves, all cards must face the same direction.
Again, a second set of eyes never hurts. If you think you see a pattern, have one of the other Judges look at it to see if he sees the same thing.
Checking the Deck: the cards
Finally, you get around to matching the cards with the decklist. Your approach may be different depending on the format. Constructed decks are far easier to check than Limited because they tend to have fewer different cards. If you've done your setup well and there are no problems with the deck, the check should take less than 10 minutes. Honing your skills, you can easily do it in five.
Some Judges prefer sorting the cards and then matching them to the list; others prefer to go with the deck as is. Sorting may be preferable in Limited, especially with multiple sets, since you're checking more sheets of paper (decklist sheets are generally provided for Limited Events). Either way, one card at a time, mark the decklist for each card that you match. Check the main deck first, and then the sideboard. Make sure that all cards you have are on the decklist and that everything on the decklist is present. If you find a discrepancy, continue checking the entire deck before taking any actions.
A deck or sideboard is illegal if it meets the following conditions: it contains an illegal number of cards, it contains cards that are illegal in the format, it contains cards that would violate a game rule (like more than the 4-card limit), or the contents of the deck don't match the decklist.
Remember that the decklist is the ultimate guide to the deck. If you find cards in the deck that aren't in the decklist or there are cards that are listed on the list but aren't in the deck, have the player fix the deck to match the contents of the list. The penalty for this at all levels is a game loss. If the player can't fix the deck within five minutes, upgrade the penalty to a match loss. If the player can't fix the deck by the beginning of the next round, the player cannot continue in the tournament.
One thing that happens frequently in Limited events where decklists are provided is players mismarking the sheet (one box above or below the card they intended to mark). Here is where a great deal of discretion on the part of the Judge is necessary, and where it helps the Judge to be familiar with the particular environment. You can generally rest assured that if the card the player actually has in his deck is deck is not as good as the card that's marked, he's simply made a decklist error. Correcting the list to match the contents of the deck is a reasonable solution.
A more difficult call to make is when the card the player is playing with is obviously better than the card that's marked (she's playing with Kavu Titan, but Kavu Lair is marked). Unless you see obvious signs of cheating (marked in different pen, the player registering the deck doesn't remember the "good card"), assume it's a clerical error and nothing more. Once again, correct the list to match the contents of the deck. I've never seen evidence of this kind of cheating in a Sealed Deck tournament.
If you're playing at REL 1 or 2 and not using decklists, have the player fix the deck so it's legal (taking out the illegal cards). If this results in the deck containing fewer than the legal number of cards, or if the deck contained fewer than the legal number of cards in the first place, then they may add only basic land (of the player's choice) to reach the legal number.
The Deck Check is a integral part of tournament Magic. It may at times become tedious, but it gives the players a sense that we're honestly concerned with the integrity of the event-which is the reason we're there in the first place. Set up the process well, and the Deck Check becomes a necessary but relatively painless part of the tournament experience.