2005 rank | 2004 rank | Institution | Country | Peer score | Citations per paper |
| 1 | 1 | Cambridge University | UK | 100 | 12.9 |
| 2 | 2 | Oxford University | UK | 94.6 | 12.2 |
| 3 | 4 | University of California, Berkeley | US | 92.7 | 16 |
| 4 | 3 | Harvard University | US | 89.9 | 20.6 |
| 5 | 5 | Massachusetts Institute Technol | US | 87.3 | 16.6 |
| 6 | 8 | Princeton University | US | 80.4 | 17.7 |
| 7 | 6 | Stanford University | US | 79.1 | 17.3 |
| 8 | 7 | Tokyo University | Japan | 74.5 | 9.2 |
| 9 | 9 | California Institute of Technology | US | 72.4 | 18 |
| 10 | 10 | Imperial College London | UK | 69.5 | 10.7 |
| 11 | 12 | Cornell University | US | 64.3 | 12.5 |
| 12 | 13 | ETH Zurich | Switzerland | 63.1 | 14 |
| 13 | 18 | Australian National University | Australia | 61.9 | 11.7 |
| 14 | 11 | Beijing University | China | 60.8 | - |
| 15 | 14 | Yale University | US | 60.1 | 16.9 |
| 16 | 15 | Kyoto University | Japan | 58.5 | 7.8 |
| 17 | 17 | University of Chicago | US | 58.3 | 16.3 |
| 18 | 19 | Ecole Normale Supérieure, Paris | France | 57 | - |
| 19 | 20 | Ecole Polytechnique | France | 54.5 | - |
| 20 | 16 | Paris VI, Pierre et Marie Curie | France | 54.2 | 8.6 |
| 21 | 25 | Lomonosov Moscow State University | Russia | 51.1 | - |
| 22 | 21 | Heidelberg University | Germany | 50.6 | 11.6 |
| 23 | 22 | University of California, Los Angeles | US | 49.3 | 13.9 |
| 24 | 36 | University of Toronto | Canada | 49 | 11 |
| 25= | 32 | University of California, Santa Barbara | US | 46.8 | 17.6 |
| 25= | 23 | University of Texas at Austin | US | 46.8 | 11.4 |
| 27 | 28 | La Sapienza University, Rome | Italy | 46.7 | 7.8 |
| 28 | 37 | Utrecht University | Netherlands | 46.3 | 10.5 |
| 29= | 27 | Munich University | Germany | 45.9 | 9.3 |
| 29= | 24 | University of Illinois | US | 45.9 | 11.2 |
| 31 | 28 | Columbia University | US | 45.8 | 15.8 |
| 32 | 30 | Melbourne University | Australia | 45 | 8.5 |
| 33 | 26 | Gottingen University | Germany | 44.7 | 8.6 |
| 34 | 35 | National University of Singapore | Singapore | 44.2 | 5.2 |
| 35 | 34 | Université Paris-Sud 11 | France | 43.3 | 9.9 |
| 36 | 31 | Indian Institutes of Technology | India | 43.2 | - |
| 37 | 67 | Sydney University | Australia | 41 | 7.8 |
| 38 | 56 | Edinburgh University | UK | 40.8 | 12.5 |
| 39 | 41 | Monash University | Australia | 40 | - |
| 40 | 69 | New South Wales University | Australia | 39.7 | 8 |
| 41 | 39 | University of Michigan | US | 39.3 | 12.6 |
| 42 | 33 | Johns Hopkins University | US | 39 | 15.5 |
| 43 | 48 | University of British Columbia | Canada | 38.7 | 10.1 |
| 44 | 64 | McGill University | Canada | 38.4 | 9.8 |
| 45= | 46 | China University of Sci & Technol | China | 38.3 | - |
| 45= | 42 | Seoul National University | South Korea | 38.3 | 5.8 |
| 47 | 39 | Aarhus University | Denmark | 36.8 | - |
| 48 | 45 | University of California, San Diego | US | 36.7 | 15.3 |
| 49 | 44 | Copenhagen University | Denmark | 36.5 | 8.7 |
| 50 | 55 | Tokyo Institute of Technology | Japan | 36.4 | - |
| 51 | 38 | National Taiwan University | Taiwan | 36.2 | 5.3 |
| 52 | 43 | Osaka University | Japan | 35.9 | 7.3 |
| 53 | 48 | Manchester University and Umist | UK | 35.6 | 9 |
| 54 | 54 | Technical University Munich | Germany | 35.5 | 11.2 |
| 55 | 52 | Tsing Hua University | China | 35.2 | - |
| 56 | 86 | Queensland University | Australia | 35 | 7 |
| 57 | 86 | Tel Aviv University | Israel | 34.9 | 9.6 |
| 58= | 61 | Technion Israel Inst of Tech | Israel | 34.8 | 7.1 |
| 58= | 57 | Tohoku University | Japan | 34.8 | 7.6 |
| 58= | 100 | Leiden University | Netherlands | 34.8 | - |
| 61= | 52 | Nanjing University | China | 34.6 | - |
| 61= | 61 | Warwick University | UK | 34.6 | - |
| 63= | 72 | Hong Kong University | Hong Kong | 34.3 | - |
| 63= | 47 | Kings College London | UK | 34.3 | - |
| 65 | 58 | University College London | UK | 34.2 | 10.3 |
| 66 | 71 | Bristol University | UK | 34 | 10.3 |
| 67 | 51 | University of Pennsylvania | US | 33.8 | 16.6 |
| 68= | 60 | Humboldt University, Berlin | Germany | 33.5 | 9 |
| 68= | 50 | Hong Kong University Sci and Tech | Hong Kong | 33.5 | - |
| 70= | 67 | Vienna University of Technology | Austria | 33.4 | - |
| 70= | 84 | Delft University of Technology | Netherlands | 33.4 | 9.3 |
| 72 | 99 | Auckland University | New Zealand | 33 | - |
| 73= | 78 | Pisa University | Italy | 32.8 | 8.2 |
| 73= | 98 | St Petersburg State University | Russia | 32.8 | - |
| 75 | 94 | Trinity College, Dublin | Ireland | 32 | - |
| 76 | 59 | Bonn University | Germany | 31.9 | 8.1 |
| 77 | 81 | Frankfurt University | Germany | 31.6 | - |
| 78= | 79 | Technical University of Berlin | Germany | 31.3 | 8.9 |
| 78= | - | University of Wisconsin | US | 31.3 | 11.7 |
| 80 | 83 | Stuttgart University | Germany | 31.1 | 8.2 |
| 81 | 61 | Vienna University | Austria | 31 | 7.7 |
| 82= | - | Boston University | US | 30.9 | - |
| 82= | 76 | State University of New York | US | 30.9 | 14.8 |
| 84 | - | Nanyang Tech University | Singapore | 30.6 | - |
| 85 | - | Brussels Free University (French) | Belgium | 30.3 | 8.9 |
| 86= | 72 | Innsbruck University | Austria | 30.1 | - |
| 86= | - | Aachen RWTH | Germany | 30.1 | 8.5 |
| 88 | 77 | Fudan University | China | 30 | - |
| 89 | - | Ecole Normale Supérieure, Lyon | France | 29.9 | - |
| 90 | - | Birmingham University | UK | 29.8 | 9.8 |
| 91= | - | Malaysia National University | Malaysia | 29.7 | - |
| 91= | 61 | Uppsala University | Sweden | 29.7 | 9.4 |
| 93 | - | National Autonomous Univ Mexico | Mexico | 29.4 | 5.5 |
| 94 | 69 | Nagoya University | Japan | 29.3 | 8.8 |
| 95 | 74 | Washington University | US | 29.2 | 15.4 |
| 96 | 95 | Durham University | UK | 28.9 | 13.5 |
| 97 | - | Hamburg University | Germany | 28.8 | 10 |
| 98= | - | Univ Louis Pasteur Strasbourg I | France | 28.7 | 12.5 |
| 98= | 91 | Hebrew University of Jerusalem | Israel | 28.7 | 8.9 |
| 98= | 75 | Penn State University | US | 28.7 | 11 |