The club champions from each of the six confederations played in a knockout tournament. The quarter-final match-ups were set up by a draw including the AFC, CAF, CONCACAF and OFC champions, while the UEFA and CONMEBOL champions were given byes to the semi-finals. The losers of the quarter-finals would play for the fifth place, while the losers of the semi-finals were to play in a third-place play-off.
A team from the host nation did not participate, as was initially proposed. Following the departure of Australia from the OFC, the Oceanian representative, Auckland City, was fully amateur, so forcing them to play a play-off for a place in the quarter-finals against the J. League champions (Gamba Osaka) was considered, which would have also promoted local interest. The change would have also eliminated the fifth-place play-off, to keep the number of games intact. This was finally rejected, but the tournament format was changed for the 2007 edition.
|Jeonbuk Hyundai Motors||AFC Champions League 2006 winners|
|FC Barcelona||UEFA Champions League 2005-06 winners|
|Club América||CONCACAF Champions' Cup 2006 winners|
|Al-Ahly||CAF Champions League 2006 winners|
|Internacional||CONMEBOL Copa Libertadores 2006 winners|
|Auckland City FC||OFC Oceania Club Championship 2006 winners|
|FIFA Club World Cup|
|Golden Ball||Silver Ball||Bronze Ball|
|Fair play||FC Barcelona|