In order to prioritise interventions for micronutrient deficiencies in China, the populations affected by iron and zinc deficiencies were assessed based on data from the 2002 China National Nutrition and Health Survey. The costs and cost-effectiveness of supplementation, food diversification and food fortification were estimated using the standard World Health Organization ingredients approach. Results indicated that 30% of children (<2 years), adults (>60 years), pregnant and lactating women, and 20% of women of reproductive age were anaemic, some 245 million people. Approximately 100 million people were affected by zinc deficiency (zinc intake inadequacy and stunting), the majority living in rural areas. Among interventions on iron and zinc deficiency, biofortification showed the lowest costs per capita, I$0.01 (international dollars), while dietary diversification through health education represented the highest costs at I$1148. The cost-effectiveness of supplementation, food fortification and dietary diversification for iron deficiency alone was I$179, I$66 and I$103 per disability-adjusted life-year (DALY), respectively. Data for biofortification were not available. For zinc deficiency, the corresponding figures were I$399, I$153 and I$103 per DALY, respectively. In conclusion, iron and zinc deficiencies are of great public health concern in China. Of the two long-term intervention strategies, i.e. dietary diversification and biofortification with improved varieties, the latter is especially feasible and cost-effective for rural populations. Supplementation and fortification can be used as short-term strategies for specific groups.