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Background: Systematic assessment of recent health research output from India, and its relation with the estimated disease burden, is not available. This information would help understand the areas in health research that need improvement in India to enhance the health of India's population. Methods: The health research output from India during 2002, which was accessible in the public domain, was assessed by searching PubMed and other internet health literature databases, and was related to the disease burden suggested by the Global Burden of Disease Study. The main outcome measures were number of health papers with abstracts in basic, clinical and public health sciences; quality-adjusted research output based on the impact factors of journals in which the papers were published; classification of papers in disease/condition categories and comparison of research output with the estimated disease burden in each category. Comparison of the health papers from India during 2002 included in PubMed was done with those from Australia during one quarter of 2002. Results: Of the 4876 health papers from India in 2002 in PubMed, 48.4%, 47.1% and 4.4% were in basic, clinical and public health sciences, respectively. Of the 4495 papers based on original research, only 3.3% were in public health. Quality-adjusted original research output was highest for non-communicable diseases (62% of total). Of the total quality-adjusted original research output, the proportions in injuries (0.7%), cardiovascular diseases (3.6%), respiratory infections (0.2%), diarrhoeal diseases (1.9%), perinatal conditions (0.4%), childhood cluster diseases (0.5%), unipolar major depression (0%), and HIV/AIDS (1.5%) were substantially lower than their proportional contribution to the disease burden in India. Human resources, health policy, health economics, and impact assessment of interventions were particularly poorly represented in public health research. The Australia-India ratio for quality-adjusted health research output per unit gross domestic product was 20 and for public health research output was 31. Conclusions: Good-quality public health research output from India is grossly inadequate, and strategic planning to improve it is necessary if substantial enhancement of population health were to be made possible. There is inordinately low relative research output in several diseases/ conditions that cause major disease burden in India. [ABSTRACT FROM AUTHOR]