The 2016 tables are based on Nature Index data from 1 January 2015 to 31 December 2015.
| 2015 | Institution | WFC 2014 | WFC 2015 |
|---|---|---|---|
| 1 | University of Lisbon (ULISBOA), Portugal | 42.8 | 31.43 |
| 2 | University of Porto (UP), Portugal | 20.38 | 17.2 |
| 3 | University of Aveiro (UA), Portugal | 12.89 | 13.97 |
| 4 | University of Coimbra (UC), Portugal | 5.33 | 12.11 |
| 5 | New University of Lisbon (UNL), Portugal | 10.08 | 11.12 |
| 6 | Gulbenkian Science Institute (IGC), Portugal | 3.48 | 7.17 |
| 7 | University of Minho (UM), Portugal | 3.46 | 6.56 |
| 8 | Champalimaud Foundation (EN), Portugal | 5.37 | 5.45 |
| 9 | International Iberian Nanotechnology Laboratory (INL), Portugal | 2.03 | 4.06 |
| 10 | University of Beira Interior (UBI), Portugal | 0.41 | 1.6 |
| 11 | INESC Microsistemas & Nanotecnologias (INESC MN), Portugal | 1.03 | 1.52 |
| 12 | Instituto de Física dos Materiais da Universidade do Porto (IFIMUP), Portugal | 1.06 | 1.11 |
| 13 | University of Algarve (UAlg), Portugal | 2.06 | 0.82 |
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