Globally, two billion people suffer from micronutrient malnutrition. Biofortification, the process of breeding staple food crops to have higher micronutrient content, has proven to be efficacious and cost-effective in addressing micronutrient malnutrition. To determine where and in which crop-micronutrient combinations to invest, a global Biofortification Prioritization Index (BPI) was developed (Asare-Marfo et al., 2013). While a country s rank in the global context is useful, it is not granular enough to develop strategies within heterogenous countries. Therefore, this paper utilizes methodology to develop a subnational-level BPI for Nigeria, a country which shows promise for biofortified crops. The subnational BPI is based on three sub-indices: production, consumption, and micronutrient deficiency. In addition, targeted areas are classified as areas of: (1) impact and intervention, (2) impact, or (3) intervention. Sensitivity analyses tested the robustness of BPI results on single sub-index parameters. For vitamin A maize s introduction, the North East and North West zones offer the most promise while the southern zones generate the greatest impact for the introduction of vitamin A cassava. Concentrating vitamin A sweet potato investments in the North Central zone is the most effective while focusing in the North West is the most promising strategy for iron pearl millet. Acknowledgement : The authors would sincerely like to thank Dr. Erick Boy, Head of the HarvestPlus Nutrition Research Unit, and Ms. Amarachi Utah for their consultation and support of this research.