OBJECTIVE: The present study aimed to estimate the health benefits of selective taxation of healthy and unhealthy food commodities in relation to CVD and nutrition-related cancers. DESIGN: The potential health effects of a selective taxation scenario were estimated as changes in the burden of disease, measured by disability-adjusted life years, from health outcomes affected by the changes in food intake. The change in burden of a disease was calculated as the change in incidence of the disease due to a modified exposure level, using the potential impact fraction. Estimates of relative risk for the associations between various foods and relevant diseases were found through a literature search and used in the calculation of potential impact fractions. SETTING: The study was based in Denmark, estimating the health effects of a Danish selective taxation scenario. SUBJECTS: The potential health effects of selective taxation were modelled for the adult Danish population. RESULTS: Halving the rate of value-added tax on fruit and vegetables and increasing the tax on fats would result in moderate reductions in the burden of disease from IHD, ischaemic stroke, and colorectal, lung and breast cancer (0·4-2·4 % change). The largest effect could be obtained through increased intake of fruit and vegetables (0·9-2·4 %). CONCLUSIONS: Applying selective taxation to healthy and unhealthy foods can moderately reduce the burden of disease in the Danish population.