Philippine Collegiate Champions League 2006–07 CCL Participating teams

| Seed | Team | League | Notes | Eliminated_at |
|---|---|---|---|---|
| 14 | José Rizal University Heavy Bombers | NCAA | NCAA 6th place - Wildcard | Semifinals (eliminated by San Beda) |
| 15 | National University Bulldogs | UAAP | UAAP 7th place - Wildcard | Round of 16 (eliminated by San Beda) |
| 16 | PMI Colleges Admirals | CUSA | CUSA champion - Wildcard | Round of 16 (eliminated by Ateneo) |