While 80 percent of MESA high school graduates attend California public institutions of higher education, many go to independent colleges and universities nationwide. Here are the top 10 independents attended by MESA students from 1998–99 through 2003–04:
| California |
Out of State |
| 1. University of the Pacific |
1. Massachusetts Institute of Technology |
| 2. University of Southern California |
2. Xavier University (New Orleans) |
| 3. University of La Verne |
3. Howard University |
| 4. Stanford University |
4. Howard University |
| 5. Loyola Marymount University |
5. Tuskegee University |
| 6. Azusa Pacific University |
6. Brown University |
| 7. St. Mary's College |
7. University of Notre Dame |
| 8. Santa Clara University |
8. Spelman College |
| 9. University of San Francisco |
9. Cornell University |
| 10. University of Redlands |
10. Yale University |
