Philippine Collegiate Champions League 2006–07 CCL Participating teams

| Seed | Team | League | Notes | Eliminated_at |
|---|---|---|---|---|
| 1 | Ateneo de Manila University Blue Eagles | UAAP | UAAP runner-up | Quarterfinals (eliminated by Mapúa) |
| 2 | San Beda College Red Lions | NCAA | NCAA champion | Finals (defeated by UE) |
| 3 | University of Santo Tomas Growling Tigers | UAAP | UAAP champion | Round of 16 (eliminated by JRU) |
| 4 | Philippine Christian University Dolphins | NCAA | NCAA runner-up | Quarterfinals (eliminated by UE) |
| 5 | University of the East Red Warriors | UAAP | UAAP 3rd place | Champions (Finals vs. San Beda) |
| 6 | Colegio de San Juan de Letran Knights | NCAA | NCAA 3rd place | Quarterfinals (eliminated by JRU) |