The Massachusetts Institute of Technology produces the highest proportion of highly cited papers, but the UK's top institution, the University of Cambridge, ranks outside the top 30.
These are the headline findings of this year's Leiden Ranking, produced by bibliometrics experts at Leiden University in the Netherlands.
The rankings draw on citations data for research papers published by 500 large research-intensive universities between 2005 and 2009. Humanities research is excluded because it not well represented in Thomson Reuters' Web of Science, from which the data are drawn.
A new flagship table, included in the Leiden Ranking for the first time this year, rates institutions according to the proportion of their English-language papers that are among the 10 per cent most cited in their fields.
Of the top 50 places, 42 are occupied by US institutions, led by MIT and Princeton and Harvard universities. More than 25 per cent of MIT papers are highly cited.
The highest ranked non-US institution is the Ecole Polytechnique Federale de Lausanne, in 12th place.
But UK institutions fare significantly worse than they do in other global rankings, such as those produced by Times Higher Education and Shanghai Jiao Tong University. Cambridge is ranked 31st, with nearly 17 per cent of its papers highly cited. The London School of Hygiene and Tropical Medicine is 33rd, the University of Oxford 36th and Durham University 42nd.
MIT keeps its place at the top of an alternative ranking based on average citation counts, adjusted for field differences and age and type of document. But Germany's University of Gottingen leaps to second. Cambridge is again the top UK representative, in 21st place.
Paul Wouters, professor of scientometrics at Leiden, said rankings based on average citation counts could be distorted by very highly cited papers, so he regarded the ranking based on highly cited papers as a preferable way to compare universities "at the global level".
He said that UK universities' weaker showing compared with other league tables was a result of the Leiden Rankings' concentration on citations data, rather than mixing it into an "arbitrary combination" of other factors such as income, reputation and "education" factors such as staff-to-student ratios.
But he noted that the UK was still second only to the US overall, with 12 universities in the top 100, measured by highly cited papers. The Netherlands was third with seven.
Harvard University produced by far the most publications between 2005 and 2009: more than 33,500. The second-most-productive institution, the University of Toronto, published just under 21,000. Cambridge, Oxford and University College London all produced about 14,000, placing them 13th, 14th and 17th respectively.
The London School of Hygiene and Tropical Medicine tops an alternative ranking based on the proportion of papers that involved collaborations. Nearly 50 per cent of its publications were internationally co-authored.