Group A
Team | GP | W | L | D | GS | GA | HG | RG | GD | P |
| Marathon | 6 | 4 | 1 | 1 | 12 | 5 | 6 | 6 | +7 | 13 |
| Cruz Azul | 6 | 3 | 2 | 1 | 8 | 4 | 7 | 1 | +4 | 10 |
| Saprissa | 6 | 3 | 2 | 1 | 7 | 9 | 5 | 2 | -2 | 10 |
| D.C. United | 6 | 0 | 5 | 1 | 4 | 13 | 2 | 2 | -9 | 1 |
Group B
Team | GP | W | L | D | GS | GA | HG | RG | GD | P |
| UNAM | 6 | 3 | 0 | 3 | 18 | 7 | 13 | 5 | +11 | 12 |
| Houston Dynamo | 6 | 2 | 1 | 3 | 9 | 9 | 4 | 5 | 0 | 9 |
| Luis Angel Firpo | 6 | 2 | 2 | 2 | 6 | 8 | 3 | 3 | -2 | 8 |
| San Francisco | 6 | 0 | 4 | 2 | 4 | 13 | 1 | 3 | -9 | 2 |
Group C
Team | GP | W | L | D | GS | GA | HG | RG | GD | P |
| Atlante | 6 | 3 | 1 | 2 | 6 | 3 | 3 | 3 | +3 | 11 |
| Montreal Impact | 6 | 3 | 1 | 2 | 10 | 5 | 3 | 7 | +5 | 11 |
| Olimpia | 6 | 2 | 2 | 2 | 10 | 6 | 6 | 4 | +4 | 8 |
| Joe Public | 6 | 1 | 5 | 0 | 3 | 15 | 2 | 1 | -12 | 3 |
Group D
Team | GP | W | L | D | GS | GA | HG | RG | GD | P |
| Santos Laguna | 6 | 3 | 2 | 1 | 14 | 11 | 9 | 5 | 3 | 10 |
| Puerto Rico Islanders | 6 | 2 | 2 | 2 | 9 | 10 | 7 | 2 | -1 | 8 |
| Tauro FC | 6 | 2 | 2 | 2 | 9 | 10 | 4 | 5 | -1 | 8 |
| Municipal | 6 | 1 | 2 | 3 | 12 | 13 | 8 | 4 | -1 | 6 |
Key: GP=Games Played; W=Wins; L=Losses; D=Draws; GS=Goals Scored; GA=Goals Allowed; HG=Home Goals; RG=Road Goals; GD=Goal Differential; P=Points
- The top two clubs from each of the four groups will advance to the Elimination Stage of the CONCACAF Champions League.
- These eight teams will be drawn into four Quarterfinal pairings to play home-and-away match-ups in February 2009.
- The four Quarterfinal winners will then play in two Semifinal home-and-away match-ups in March and April 2009 with the two Semifinal winners squaring-off in the home-and-away CONCACAF Champions League Final in late April 2009.
- The CONCACAF Champions League winner will qualify as the CONCACAF representative to the 2009 edition of the FIFA Club World Cup.
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