Health policies entail consequences in multiple domains. Fundamentally, they increase intervention uptake and consequent health gains (e.g. mortality and morbidity averted). In addition, they can generate non-health benefits including, for example, the enhancement of equity (e.g. equalization of health among individuals in a given population), and financial consequences for households like eliminating private expenditures and the provision of financial risk protection and poverty reduction. Traditionally, health economic evaluations (cost-effectiveness analysis, CEA) have focused on estimating an intervention cost per health gain (e.g. dollar per life year gained). Extended cost-effectiveness analysis (ECEA) supplements CEA with non-health benefits (e.g. equity, poverty reduction) evaluation. ECEA enables the inclusion of multiple criteria including equity criteria into decision-making for selecting health policies. We describe how ECEA can help develop priority health system modeling research areas to identify good value for money investments in health system strengthening.