As was the case for the 2006 tournament, the sixteen teams have been split into four pools of four teams each. Whereas previously the teams played in round-robin competition in the first and second rounds, this time they will take part in a double-elimination format, meaning that teams are only guaranteed of playing two games. This change was made to eliminate the complicated tiebreaking procedures, which were required for one of the pools in each of the first and second rounds in 2006.
After the first round, the tournament will be held on American soil. The top two teams from each of the four pools - seeded from the final game in their respective pools - will progress to the second round, with the teams from Pools A and B meeting at PETCO Park in San Diego, California for Pool 1, and the teams in Pools C and D playing at Dolphin Stadium in Miami Gardens, Florida for Pool 2. Again, both pools will make use of double-elimination to determine the teams qualifying for the semi finals. In another change from 2006, the four qualifying teams will cross over for the semi finals, with the winner of each pool playing against the runner-up from the other pool. The finals process is otherwise unchanged, with each semi final being a single elimination match, with the victors meeting in the final to determine the champions. All three final games are to be held at Dodger Stadium in Los Angeles, California. 
Tickets went on sale in November for all games, and were sold in strips for entire venues. Ticket prices ranged from $60 for the opening round to $1500 for the final round. Single game seats went on sale in February 2009.
As was the case for the 2006 Classic, several rules have been announced for the 2009 tournament that modify the existing rules for international baseball set out by the IBAF.
Once again there will be limits on the number of pitches thrown in a game, though the limits themselves have changed from the inaugural tournament:
70 pitches in round 1 (up from 65 in '06)
85 pitches in round 2 (up from 80)
100 pitches in the semi finals and final (up from 95)
If a pitcher reaches their limit during an at bat, they are allowed to finish pitching to the batter, but must be removed from the game and the end of the at bat.
Any pitcher who makes 30 or more pitches in a game is ineligible to pitch on the following day. As the semi finals and final are played over three consecutive days, a so-called "pitcher rest equalization" rule has been added: a pitcher making 30 or more pitches in a semi final is ineligible to pitch in the final. This negates an advantage the winners of the first semi final would have in the final.
Instant replay will also be available to umpires during the tournament. As was introduced in Major League Baseball during the 2008 season, replays can only be used to adjudicate on home run decisions, to determine whether the ball was fair or foul, over the fence or not, and the impact of fan interference.
An alternative version of the IBAF's extra inning rule will also be introduced. If after 12 innings the score is still tied, each half inning thereafter will start with runners on second and first base. The runners will be the eighth and ninth hitters due in that inning respectively. For example, if the number five hitter is due to lead off the inning, the number three hitter would be on second base, and the number four hitter on first base. Whether this rule will be used in the final is still to be determined by the WBC Rules and Regulations Committee.
All base coaches will be required to wear protective helmets, and participating teams will be required to announce the next day's starting pitcher.
In the United States, ESPN and the MLB Network will share the rights, with ESPN broadcasting 23 of the games, including the semi-finals and final, while MLB Network will show the remaining 16. Internationally, it will be broadcast to 167 countries by ESPN International.