BACKGROUND: Recommendations to tackle major health problems such as childhood obesity may not be appropriate if they fail to take account of the prevailing socio-political, cultural and economic context. We describe the development and application of a qualitative risk analysis approach to identify non-scientific considerations framing the policy response to obesity in Denmark and Latvia. METHODS: Interviews conducted with key stakeholders in Denmark and Latvia, undertaken following a review of relevant literature on obesity and national policies. A qualitative risk analysis model was developed to help explain the findings in the light of national context. RESULTS: Non-scientific considerations that appeared to influence the response to obesity include the perceived relative importance of childhood obesity; the nature of stakeholder relations and its impact on decision-making; the place of obesity on the policy agenda; the legitimacy of the state to act for population health and views on alliances between public and private sectors. CONCLUSION: Better recognition of the exogenous factors affecting policy-making may lead to a more adequate policy response. The development and use of a qualitative risk analysis model enabled a better understanding of the contextual factors and processes influencing the response to childhood obesity in each country.