Health research is crucial to understand a country’s needs and to improve health outcomes. We conducted a scoping review and analysis of existing health data in Timor-Leste to identify the health research priorities of the country. Published and unpublished health research in Timor-Leste from 2001 to 2011 that reported objectives, methods and results were identified. Key findings were triangulated with data from national surveys and the Health Management Information System; 114 eligible articles were included in the analysis, the leading topics of which were communicable (malaria, tuberculosis, HIV and sexually transmitted diseases and dengue) and non-communicable (eye and mental health) diseases. There were 28 papers (25%) on safe motherhood, child health and nutrition, of which 20 (71%) were unpublished. The review of national indicators showed high infant, under-five and maternal mortality rates. Burden of disease is greatest in young children, with respiratory infections, febrile illnesses and diarrheal disease predominating. There is poor access to and utilization of health care. Childhood malnutrition is an important unresolved national health issue. There are several obstacles leading to under-utilization of health services. The following topics for future health research are suggested from the review: nutrition, safe motherhood, childhood illness (in particular identifying the causes and cause-specific burden of severe respiratory, febrile and diarrheal diseases) and access to and use of health services.