The most important public health priority in agricultural policy-making is currently food safety, despite the relatively higher importance of food security, nutrition, and other agricultural-related health issues in terms of global burden of disease. There is limited experience worldwide of using health impact assessment (HIA) during the development of agriculture and food policies, which perhaps reflects the complex nature of this policy sector. This paper presents methods of HIA used in the Republic of Slovenia, which is conducting a HIA of proposed agricultural and food policies due to its accession to the European Union. It is the first time that any government has attempted to assess the health effects of agricultural policy at a national level. The HIA has basically followed a six-stage process: policy analysis; rapid appraisal workshops with stakeholders from a range of backgrounds; review of research evidence relevant to the agricultural policy; analysis of Slovenian data for key health-related indicators; a report on the findings to a key cross-government group; and evaluation. The experience in Slovenia shows that the HIA process has been a useful mechanism for raising broader public health issues on the agricultural policy agenda, and it has already had positive results for policy formation. HIA is one useful approach to more integrated policy-making across sectors, but clearly it is not the only mechanism to achieve this. A comparison of the approach used in Slovenia with HIA methods in other countries and policy contexts shows that there are still many limitations with HIA application at a government level. Lessons can be learnt from these case studies for future development and application of HIA that is more relevant to policy-makers, and assists them in making more healthy policy choices.