BACKGROUND: Poverty is highly concentrated in countries affected by armed conflict which are the furthest from reaching the Millennium Development Goals. Tracking aid patterns for health is crucial for improving the effectiveness of external aid to countries affected by armed conflict which tend to depend heavily upon external assistance and also have particularly acute health needs. OBJECTIVES: This study systematically assesses the reliability of global aid databases which are commonly used for tracking aid to countries affected by armed conflict. It offers analyses of two main databases - the Creditor Reporting System (CRS) and the Financial Tracking System (FTS) by reviewing the strengths and weaknesses of these data sources. METHODS: A literature review was conducted to assess the existing evidence on aid tracking generally, and aid databases more broadly. Interviews were also conducted with experts involved in health resource tracking, donor agencies, and NGOs. RESULTS: Despite limitations, the CRS and FTS are appropriate for tracking aid for conflict-affected countries as they are comprehensive and allow analysis of different aid activities, countries, years, and donors. CONCLUSIONS: The study offers recommendations on how CRS and FTS might be enhanced to try and improve the accountability and effectiveness of aid to countries affected by armed conflict.