The league table is once again dominated by US institutions, with Harvard followed by the University of California, Berkeley second and Stanford University third.
Eight of the top 10 institutions are American, with the University of Cambridge (fifth) and University of Oxford (10th) flying the flag for the rest of the world.
While widely respected, the Shanghai Jiao Tong ranking is based almost entirely on scientific research strength, in contrast to the upcoming Times Higher Education World University Rankings, which will offer a broader overview of universities' strengths.
The THE rankings have been overhauled for 2010, with the old methodology replaced by a new, more rigorous approach and all data supplied by Thomson Reuters. Among the changes is a 30 per cent weighting for a new "teaching and learning environment" measure, including the first teaching reputation score in the global ranking field.
In the Shanghai Jiao Tong table, which was published last week, the highest non-US institution other than Cambridge and Oxford is the University of Tokyo in 20th place.
The top-rated institution from mainland Europe is the Swiss Federal Institute of Technology Zurich (23rd), while the Australian National University is the country's highest flyer (59th). No Chinese institutions make the top 100.
The other UK institutions to make the list are: University College London (21st), Imperial College London (26th), the University of Manchester (44th), the University of Edinburgh (54th), King's College London (63rd), the University of Bristol (66th), the University of Nottingham (84th), the University of Sheffield (88th) and the University of Birmingham (99th). More than half of the top 100 - 54 institutions - are in the US, 10 are in the UK, 23 in mainland Europe, nine in the Asia Pacific region and four in Canada.
SHANGHAI JIAO TONG TOP 10
1. Harvard University
2. University of California, Berkeley
3. Stanford University
4. Massachusetts Institute of Technology
5. University of Cambridge
6. California Institute of Technology
7. Princeton University
8. Columbia University
9. University of Chicago
10. University of Oxford