Abstract Background Personalized prevention and pharmacogenomics are emerging fields in global health, promoting tailored approaches to disease prevention and individualized drug therapy, based on the individuals’ genetic profile. However, adoption of these technologies in public health is challenged by the possibility of health disparities. Health Impact Assessment (HIA) is a useful tool to address this issue, by examining how policies differentially impact population groups, guiding stakeholders to more equitable and inclusive outcomes. Solid frameworks for assessing health impacts are needed to avoid heterogeneity when accounting for equity outcomes in HIA. This study tested a conceptual model for HIA in personalized medicine, using a case study in pharmacogenetics to map potential impacts and outcomes, with a focus on health equity. Methods A conceptual model for a HIA was developed to map expected impacts and outcomes of a health policy, aimed at enforcing DPYD genotype-guided dosing to prevent fluoropyrimidine toxicity in colorectal cancer patients. The conceptual model was developed based on literature reviews and consultation with stakeholders. Identification of relevant impacts guided selection of indicators and quantitative impact assessment using a Markov chain model. Results Impact pathways were identified using a three-tiered reference framework encompassing individual and population perspectives, organizational factors, and overarching health system considerations. The final diagram outlined key outcomes in four categories: health, organizational, economic and equity. HIA projections using this model were obtained for the DPYD testing policy. Conclusions In the rise of personalized medicine and pharmacogenomics, health inequalities challenges need to be addressed before implementation in healthcare. This study provided a novel HIA conceptual model for personalized prevention policies based on genomic information, with an emphasis on equity. Key messages • HIA is an adequate tool to evaluate potential health inequalities resulting from personalized medicine policies in healthcare. • This study provides a validated framework for HIA of personalized prevention policies grounded in genomic data.