Aim This paper aims to identify health research priorities that could improve the rate of progress in reducing global neonatal mortality from preterm birth and low birth weight (PB/LBW), as set out in the UN's Millennium Development Goal 4. Methods We applied the Child Health and Nutrition Research Initiative (CHNRI) methodology for setting priorities in health research investments. In the process coordinated by the World Health Organization in 2007-2008, 21 researchers with interest in child, maternal and newborn health suggested 82 research ideas that spanned across the broad spectrum of epidemiological research, health policy and systems research, improvement of existing interventions and development of new interventions. The 82 research questions were then assessed for answerability, effectiveness, deliverability, maximum potential for mortality reduction and the effect on equity using the CHNRI method. Results The top 10 identified research priorities were dominated by health systems and policy research questions (eg, identification of LBW infants born at home within 24-48 hours of birth for additional care; approaches to improve quality of care of LBW infants in health facilities; identification of barriers to optimal home care practices including care seeking; and approaches to increase the use of antenatal corticosteriods in preterm labor and to improve access to hospital care for LBW infants). These were followed by priorities for improvement of the existing interventions (eg, early initiation of breastfeeding, including feeding mode and techniques for those unable to suckle directly from the breast; improved cord care, such as chlorhexidine application; and alternative methods to Kangaroo Mother Care (KMC) to keep LBW infants warm in community settings). The highest-ranked epidemiological question suggested improving criteria for identifying LBW infants who need to be cared for in a hospital. Among the new interventions, the greatest support was shown for the development of new simple and effective interventions for providing thermal care to LBW infants, if KMC is not acceptable to the mother. Conclusion The context for this exercise was set within the MDG4, requiring an urgent and rapid progress in mortality reduction from low birth weight, rather than identifying long-term strategic solutions of the greatest potential. In a short-term context, the health policy and systems research to improve access and coverage by the existing interventions, coupled with further research to improve effectiveness, deliverability and acceptance of existing interventions, and epidemiological research to address the key gaps in knowledge, were all highlighted as research priorities.