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Research papers published by Chinese and Indian researchers during 1998-2007 and cited at least 100 times by end of 2009 are analysed. There were 776 papers with at least one author from India (amounting to 0.32% of all papers from India) and 2260 papers with at least one author from China (0.4% of all papers from China) that have gone on to be cited at least 100 times. We have identified prominent authors and institutions, journals used and fields of research. Although highly cited Chinese papers were cited on average less often than the highly cited papers from India, Chinese authors have been able to place their papers in high impact journals such as Nature and Science far more often than Indian authors. The Indian Institute of Science, Bangalore, Tata Institute of Fundamental Research, Mumbai and Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore are the prominent Indian institutions, whereas universities in Hong Kong, Peking University, Tshing Hua University and several institutions under the Chinese Academy of Science dominate in China. In terms of citations, Chinese National Human Genome Centre Shanghai, Shanghai, tops the list. [ABSTRACT FROM AUTHOR]