Scientists initiated the project 'Health system analysis to support capacity development to respond to pandemic influenza in Asia' (ASIAFLUCAP) to provide a strategic framework and to apply it to four pandemic scenarios in six Asian countries. With funding from the EU and the Rockefeller Foundation, and building on an innovative pilot research project in Thailand, scientists linked quantitative analyses of resource gaps with qualitative assessments of governance constraints. They developed a toolkit for rapid situational analysis of current capacity and future requirements that combines accurate and valid results with simple, fast and cost-effective methodology. Data collection and fieldwork enabled the identification of important health system structures and processes associated with preparedness. In fact, the health system context strongly affected pandemic preparedness programmes relating to governance and stewardship, resources and service provision. While major investments in surveillance, laboratory capabilities and public communication have improved readiness, low investment in clinical care is a major obstacle. ASIAFLUCAP also identified key health system resources required to contain and mitigate influenza and respiratory disease pandemics in each region. Scientists then conducted fieldwork to quantify real resources, including stock and core supplies from hospitals up to the national level. Using data from the H1N1/2009 influenza pandemic, ASIAFLUCAP produced a user-friendly decision support system for policymakers to make evidence-based decisions regarding resource allocation for decreased mortality. Since pandemic preparedness is not only a matter of resources but also of human-driven political processes, ASIAFLUCAP also analysed the H1N1/2009 response to identify stakeholder strengths and weaknesses to improve the governance framework and processes. ASIAFLUCAP has provided valuable knowledge leading to numerous improvements in operational capacity in all countries studied. Outcomes also spawned collaborations and project proposals with other reputed research centres from project countries.