BACKGROUND: Reproductive health needs are particularly acute in countries affected by armed conflict. Reliable information on aid investment for reproductive health in these countries is essential for improving the efficiency and effectiveness of aid. The purpose of this study was to analyse official development assistance (ODA) for reproductive health activities in conflict-affected countries from 2003 to 2006. METHODS AND FINDINGS: The Creditor Reporting System and the Financial Tracking System databases were the chosen data sources for the study. ODA disbursement for reproductive health activities to 18 conflict-affected countries was analysed for 2003, 2004, 2005, and 2006. An average of US $20.8 billion in total ODA was disbursed annually to the 18 conflict-affected countries between 2003 and 2006, of which US $509.3 million (2.4%) was allocated to reproductive health. This represents an annual average of US $1.30 disbursed per capita in the 18 sampled countries for reproductive health activities. Non-conflict-affected least-developed countries received 53.3% more ODA for reproductive health activities than conflict-affected least-developed countries, despite the latter generally having greater reproductive health needs. ODA disbursed for HIV/AIDS prevention and treatment increased by 119.4% from 2003 to 2006. The ODA disbursed for other direct reproductive health activities declined by 35.9% over the same period. CONCLUSIONS: This study provides evidence of inequity in disbursement of reproductive health ODA between conflict-affected countries and non-conflict-affected countries, and between different reproductive health activities. These findings and the study's recommendations seek to support initiatives to make aid financing more responsive to need in the context of armed conflict.